Merge pull request #8 from rasmusthog/rasmus_xanes_interactive

Rasmus xanes interactive

nafuma/auxillary.py

@@ -12,11 +12,21 @@ def update_options(options, required_options, default_options):
 
     return options
 
-def save_options(options, path):
+def save_options(options, path, ignore=None):
     ''' Saves any options dictionary to a JSON-file in the specified path'''
 
+    options_copy = options.copy()
+
+    if ignore:
+        if not isinstance(ignore, list):
+            ignore = [ignore]
+
+        for i in ignore:
+            options_copy[i] = 'Removed'
+
+
     with open(path, 'w') as f:
-        json.dump(options,f)
+        json.dump(options_copy,f, skipkeys=True, indent=4)
 
 
 def load_options(path):

nafuma/xanes/__init__.py

@@ -1 +1 @@
-from . import io, calib
+from . import io, calib, edges

nafuma/xanes/calib.py

@@ -5,10 +5,13 @@ import numpy as np
 import os
 import matplotlib.pyplot as plt
 import nafuma.auxillary as aux
+import nafuma.plotting as btp
 import nafuma.xanes as xas
 import nafuma.xanes.io as io
 from scipy.signal import savgol_filter
 from datetime import datetime
+import ipywidgets as widgets
+from IPython.display import display
 
 
 ##Better to make a new function that loops through the files, and performing the split_xanes_scan on
@@ -43,13 +46,19 @@ def pre_edge_fit(data: dict, options={}) -> pd.DataFrame:
 
     # FIXME Add log-file
 
-    required_options = ['pre_edge_start', 'log', 'logfile', 'save_plots', 'save_folder']
+    required_options = ['pre_edge_limits', 'pre_edge_masks', 'pre_edge_polyorder', 'pre_edge_store_data', 'log', 'logfile', 'show_plots', 'save_plots', 'save_folder', 'ylim', 'interactive']
     default_options = {
-        'pre_edge_start': None,
+        'pre_edge_limits': [None, None],
+        'pre_edge_masks': [],
+        'pre_edge_polyorder': 1,
+        'pre_edge_store_data': False,
         'log': False,
         'logfile': f'{datetime.now().strftime("%Y-%m-%d-%H-%M-%S")}_pre_edge_fit.log',
+        'show_plots': False,
         'save_plots': False,
-        'save_folder': './'
+        'save_folder': './',
+        'ylim': [None, None],
+        'interactive': False
     }
 
     options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
@@ -57,23 +66,40 @@ def pre_edge_fit(data: dict, options={}) -> pd.DataFrame:
     if options['log']:
         aux.write_log(message='Starting pre edge fit', options=options)
 
-
-
     # FIXME Implement with finding accurate edge position
     # FIXME Allow specification of start of pre-edge area
     # Find the cutoff point at which the edge starts - everything to the LEFT of this point will be used in the pre edge function fit
-    if not options['pre_edge_start']:
+    if not options['pre_edge_limits'][0]:
+        options['pre_edge_limits'][0] = data['xanes_data_original']['ZapEnergy'].min()
+
+    
+    if not options['pre_edge_limits'][1]:
         pre_edge_limit_offset = 0.03
 
         data['edge'] = find_element(data)
 
         edge_position = estimate_edge_position(data, options, index=0)
-        pre_edge_limit = edge_position - pre_edge_limit_offset
+        options['pre_edge_limits'][1] = edge_position - pre_edge_limit_offset
+
+    # Start inteactive session with ipywidgets. Disables options['interactive'] in order for the interactive loop to not start another interactive session
+    if options['interactive']:
+        options['interactive'] = False
+        options['interactive_session_active'] = True
+        options['show_plots'] = True
+        pre_edge_fit_interactive(data=data, options=options)
+        return
+
+
 
     # FIXME There should be an option to specify the interval in which to fit the background - now it is taking everything to the left of edge_start parameter, but if there are some artifacts in this area, it should be possible to
     # limit the interval
     # Making a dataframe only containing the rows that are included in the background subtraction (points lower than where the edge start is defined)
-    pre_edge_data = data['xanes_data_original'].loc[data['xanes_data_original']["ZapEnergy"] < pre_edge_limit]
+    pre_edge_data = data['xanes_data_original'].loc[(data['xanes_data_original']["ZapEnergy"] > options['pre_edge_limits'][0]) & (data['xanes_data_original']["ZapEnergy"] < options['pre_edge_limits'][1])].copy()
+
+    for mask in options['pre_edge_masks']:
+        pre_edge_data.loc[(pre_edge_data['ZapEnergy'] > mask[0]) & (pre_edge_data['ZapEnergy'] < mask[1])] = np.nan
+
+    pre_edge_data = pre_edge_data.dropna()
 
     # Making a new dataframe, with only the ZapEnergies as the first column -> will be filled to include the background data
     pre_edge_fit_data = pd.DataFrame(data['xanes_data_original']["ZapEnergy"])
@@ -85,7 +111,7 @@ def pre_edge_fit(data: dict, options={}) -> pd.DataFrame:
             aux.write_log(message=f'Fitting background on {os.path.basename(filename)} ({i+1}/{len(data["path"])})', options=options)
 
         #Fitting linear function to the background
-        params = np.polyfit(pre_edge_data["ZapEnergy"],pre_edge_data[filename],1)
+        params = np.polyfit(pre_edge_data["ZapEnergy"],pre_edge_data[filename],options['pre_edge_polyorder'])
         fit_function = np.poly1d(params)
 
         data['pre_edge_params'][filename] = params
@@ -96,18 +122,22 @@ def pre_edge_fit(data: dict, options={}) -> pd.DataFrame:
         #adding a new column in df_background with the y-values of the background
         pre_edge_fit_data.insert(1,filename,background) 
         
-        if options['save_plots']:
+        if options['show_plots'] or options['save_plots']:
-            if not os.path.isdir(options['save_folder']):
+            fig, (ax1, ax2) = plt.subplots(1,2,figsize=(20,10))
-                os.makedirs(options['save_folder'])
-
-            dst = os.path.join(options['save_folder'], os.path.basename(filename)) + '_pre_edge_fit.png'
-
-            fig, (ax1, ax2) = plt.subplots(1,2,figsize=(10,5))
             data['xanes_data_original'].plot(x='ZapEnergy', y=filename, color='black', ax=ax1)
             pre_edge_fit_data.plot(x='ZapEnergy', y=filename, color='red', ax=ax1)
             ax1.axvline(x = max(pre_edge_data['ZapEnergy']), ls='--')
+            ax1.axvline(x = min(pre_edge_data['ZapEnergy']), ls='--')
             ax1.set_title(f'{os.path.basename(filename)} - Full view', size=20)
             
+            if options['ylim'][0] != None:
+                ax1.set_ylim(bottom=options['ylim'][0])
+            if options['ylim'][1]:
+                ax1.set_ylim(top=options['ylim'][1])
+
+            for mask in options['pre_edge_masks']:
+                ax1.fill_between(x=mask, y1=0, y2=data['xanes_data_original'][filename].max()*2, alpha=0.2, color='black')
+
             data['xanes_data_original'].plot(x='ZapEnergy', y=filename, color='black', ax=ax2)
             pre_edge_fit_data.plot(x='ZapEnergy', y=filename, color='red', ax=ax2)
             ax2.axvline(x = max(pre_edge_data['ZapEnergy']), ls='--')
@@ -115,26 +145,53 @@ def pre_edge_fit(data: dict, options={}) -> pd.DataFrame:
             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)
 
+            if options['save_plots']:
+                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'
                 plt.savefig(dst, transparent=False)
+            
+            if not options['show_plots']:
                 plt.close()
 
 
     if options['log']:
         aux.write_log(message=f'Pre edge fitting done.', options=options)
 
+    if options['pre_edge_store_data']:
+        data['pre_edge_fit_data'] = pre_edge_fit_data
+
     return pre_edge_fit_data
 
 
 
+def pre_edge_fit_interactive(data: dict, options: dict) -> None:
+
+
+    w = widgets.interactive(
+        btp.ipywidgets_update, func=widgets.fixed(pre_edge_fit), data=widgets.fixed(data), options=widgets.fixed(options), 
+        pre_edge_limits=widgets.FloatRangeSlider(value=[options['pre_edge_limits'][0], options['pre_edge_limits'][1]], min=data['xanes_data_original']['ZapEnergy'].min(), max=data['xanes_data_original']['ZapEnergy'].max(), step=0.001),
+        pre_edge_store_data=widgets.Checkbox(value=options['pre_edge_store_data'])
+    )
+    
+    options['widget'] = w
+
+    display(w)
+
+
+
+
 def pre_edge_subtraction(data: dict, options={}):
 
-    required_options = ['log', 'logfile', 'save_plots', 'save_folder']
+    required_options = ['log', 'logfile', 'show_plots', 'save_plots', 'save_folder', 'pre_edge_subtraction_store_data']
     default_options = {
         'log': False,
         'logfile': f'{datetime.now().strftime("%Y-%m-%d-%H-%M-%S")}_pre_edge_subtraction.log',
+        'show_plots': False,
         'save_plots': False,
-        'save_folder': './'
+        'save_folder': './',
+        'pre_edge_subtraction_store_data': False
     }
 
     options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
@@ -149,20 +206,29 @@ def pre_edge_subtraction(data: dict, options={}):
 
         xanes_data_bkgd_subtracted.insert(1, filename, data['xanes_data_original'][filename] - data['pre_edge_fit_data'][filename])
 
+        if options['save_plots'] or options['show_plots']:
+
+
+                fig, ax = plt.subplots(figsize=(10,5))
+                data['xanes_data_original'].plot(x='ZapEnergy', y=filename, color='black', ax=ax, label='Original data')
+                xanes_data_bkgd_subtracted.plot(x='ZapEnergy', y=filename, color='red', ax=ax, label='Pre edge subtracted')
+                ax.set_title(f'{os.path.basename(filename)} - After subtraction', size=20)
+
+                
                 if options['save_plots']:
                     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_subtraction.png'
 
-                fig, ax = plt.subplots(figsize=(10,5))
-                data['xanes_data_original'].plot(x='ZapEnergy', y=filename, color='black', ax=ax)
-                xanes_data_bkgd_subtracted.plot(x='ZapEnergy', y=filename, color='red', ax=ax)
-                ax.set_title(f'{os.path.basename(filename)} - After subtraction', size=20)
-
                     plt.savefig(dst)
+
+                if not options['show_plots']:    
                     plt.close()
 
+    if options['pre_edge_subtraction_store_data']:
+        data['xanes_data'] = xanes_data_bkgd_subtracted
+
     return xanes_data_bkgd_subtracted
 
 
@@ -170,31 +236,57 @@ def pre_edge_subtraction(data: dict, options={}):
 
 
 def post_edge_fit(data: dict, options={}):
-    #FIXME should be called "fitting post edge" (normalization is not done here, need edge shift position)
+    ''' Fit the post edge within the post_edge.limits to a polynomial of post_edge.polyorder order. Allows interactive plotting, as well as showing static plots and saving plots to drive.
-    required_options = ['log', 'logfile', 'post_edge_interval']
+    
+    Requires data to have already been read to data['xanes_data_original'] 
+    '''
+    
+    
+    required_options = ['log', 'logfile', 'post_edge_masks', 'post_edge_limits', 'post_edge_polyorder', 'post_edge_store_data', 'interactive', 'show_plots', 'save_plots', 'save_folder']
     default_options = {
         'log': False, 
         'logfile': f'{datetime.now().strftime("%Y-%m-%d-%H-%M-%S")}_post_edge_fit.log',
-        'post_edge_interval': [None, None],
+        'post_edge_limits': [None, None],
+        'post_edge_masks': [],
+        'post_edge_polyorder': 2,
+        'post_edge_store_data': False,
+        'interactive': False,
+        'show_plots': False,
+        'save_plots': False,
+        'save_folder': './',
+        'ylim': [None, None]
     }
     options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
 
 
-    if not options['post_edge_interval'][0]:
+    if not options['post_edge_limits'][0]:
         post_edge_limit_offset = 0.03
 
         data['edge'] = find_element(data)
 
         edge_position = estimate_edge_position(data, options, index=0)
-        options['post_edge_interval'][0] = edge_position + post_edge_limit_offset
+        options['post_edge_limits'][0] = edge_position + post_edge_limit_offset
 
 
-    if not options['post_edge_interval'][1]:
+    if not options['post_edge_limits'][1]:
-        options['post_edge_interval'][1] = data['xanes_data_original']['ZapEnergy'].max()
+        options['post_edge_limits'][1] = data['xanes_data_original']['ZapEnergy'].max()
+
+    # Start inteactive session with ipywidgets. Disables options['interactive'] in order for the interactive loop to not start another interactive session
+    if options['interactive']:
+        options['interactive'] = False
+        options['interactive_session_active'] = True
+        options['show_plots'] = True
+        post_edge_fit_interactive(data=data, options=options)
+        return
 
 
-    post_edge_data = data['xanes_data_original'].loc[(data['xanes_data_original']["ZapEnergy"] > options['post_edge_interval'][0]) & (data['xanes_data_original']["ZapEnergy"] < options['post_edge_interval'][1])]
+
-    post_edge_data.dropna(inplace=True) #Removing all indexes without any value, as some of the data sets misses the few last data points and fucks up the fit
+    post_edge_data = data['xanes_data_original'].loc[(data['xanes_data_original']["ZapEnergy"] > options['post_edge_limits'][0]) & (data['xanes_data_original']["ZapEnergy"] < options['post_edge_limits'][1])].copy()
+
+    for mask in options['post_edge_masks']:
+        post_edge_data.loc[(post_edge_data['ZapEnergy'] > mask[0]) & (post_edge_data['ZapEnergy'] < mask[1])] = np.nan
+
+    post_edge_data = post_edge_data.dropna() #Removing all indexes without any value, as some of the data sets misses the few last data points and fucks up the fit
 
     # Making a new dataframe, with only the ZapEnergies as the first column -> will be filled to include the background data
     post_edge_fit_data = pd.DataFrame(data['xanes_data_original']["ZapEnergy"])
@@ -203,12 +295,15 @@ def post_edge_fit(data: dict, options={}):
     
     for i, filename in enumerate(data['path']):
         if options['log']:
-            aux.write_log(message=f'Fitting post edge on {os.path.basename(filename)} ({i+1} / {len(data["path"])})', options=options)
+            aux.write_log(message=f'Fitting post edge on {os.path.basename(filename)} ({i+1} / {len(data["path"])}) with polynomial order {options["post_edge_polyorder"]}', options=options)
 
         #Fitting linear function to the background
-        params = np.polyfit(post_edge_data["ZapEnergy"], post_edge_data[filename], 2)
+        params = np.polyfit(post_edge_data["ZapEnergy"], post_edge_data[filename], options['post_edge_polyorder'])
         fit_function = np.poly1d(params)
 
+        if options['log']:
+            aux.write_log(message=f'Post edge fitted with parameters: {params}')
+
         data['post_edge_params'][filename] = params
         
         #making a list, y_pre,so the background will be applied to all ZapEnergy-values
@@ -217,18 +312,24 @@ def post_edge_fit(data: dict, options={}):
         #adding a new column in df_background with the y-values of the background
         post_edge_fit_data.insert(1,filename,background) 
         
-        if options['save_plots']:
+        if options['save_plots'] or options['show_plots']:
-            if not os.path.isdir(options['save_folder']):
-                os.makedirs(options['save_folder'])
 
-            dst = os.path.join(options['save_folder'], os.path.basename(filename)) + '_post_edge_fit.png'
 
-            fig, (ax1, ax2) = plt.subplots(1,2,figsize=(10,5))
+            fig, (ax1, ax2) = plt.subplots(1,2,figsize=(20,10))
             data['xanes_data_original'].plot(x='ZapEnergy', y=filename, color='black', ax=ax1)
             post_edge_fit_data.plot(x='ZapEnergy', y=filename, color='red', ax=ax1)
             ax1.axvline(x = max(post_edge_data['ZapEnergy']), ls='--')
+            ax1.axvline(x = min(post_edge_data['ZapEnergy']), ls='--')
             ax1.set_title(f'{os.path.basename(filename)} - Full view', size=20)
 
+            for mask in options['post_edge_masks']:
+                ax1.fill_between(x=mask, y1=0, y2=data['xanes_data_original'][filename].max()*2, alpha=0.2, color='black')
+
+            if options['ylim'][0] != None:
+                ax1.set_ylim(bottom=options['ylim'][0])
+            if options['ylim'][1] != None:
+                ax1.set_ylim(top=options['ylim'][1])
+
             data['xanes_data_original'].plot(x='ZapEnergy', y=filename, color='black', ax=ax2)
             post_edge_fit_data.plot(x='ZapEnergy', y=filename, color='red', ax=ax2)
             ax2.axvline(x = max(post_edge_data['ZapEnergy']), ls='--')
@@ -236,84 +337,171 @@ def post_edge_fit(data: dict, options={}):
             ax2.set_ylim([min(post_edge_data[filename]), max(post_edge_data[filename])])
             ax2.set_title(f'{os.path.basename(filename)} - Fit region', size=20)
 
+            if options['save_plots']:
+                if not os.path.isdir(options['save_folder']):
+                    os.makedirs(options['save_folder'])
+
+                dst = os.path.join(options['save_folder'], os.path.basename(filename)) + '_post_edge_fit.png'
 
                 plt.savefig(dst, transparent=False)
+            
+            if not options['show_plots']:
                 plt.close()
 
 
+    if options['log']:
+        aux.write_log(message='Post edge fitting done!', options=options)
+
+    if options['post_edge_store_data']:
+        data['post_edge_fit_data'] = post_edge_fit_data
+
+
     return post_edge_fit_data
 
+
+def post_edge_fit_interactive(data: dict, options: dict) -> None:
+    ''' Defines the widgets to use with the ipywidgets interactive mode and calls the update function found in btp.ipywidgets. '''
+
+    w = widgets.interactive(
+        btp.ipywidgets_update, func=widgets.fixed(post_edge_fit), data=widgets.fixed(data), options=widgets.fixed(options), 
+        post_edge_limits=widgets.FloatRangeSlider(value=[options['post_edge_limits'][0], options['post_edge_limits'][1]], min=data['xanes_data_original']['ZapEnergy'].min(), max=data['xanes_data_original']['ZapEnergy'].max(), step=0.001),
+        post_edge_store_data=widgets.Checkbox(value=options['post_edge_store_data'])
+    )
+    
+    options['widget'] = w
+
+    display(w)
+
 def smoothing(data: dict, options={}):
 
     # FIXME Add logging
     # FIXME Add saving of files
 
-    required_options = ['log', 'logfile', 'window_length','polyorder', 'save_default']
+    required_options = ['log', 'logfile', 'show_plots', 'save_plots', 'save_folder', 'interactive', 'smooth_window_length', 'smooth_algorithm', 'smooth_polyorder', 'smooth_save_default', 'smooth_store_data']
     default_options = {
         'log': False,
         'logfile': f'{datetime.now().strftime("%Y-%m-%d-%H-%M-%S")}_smoothing.log',
+        'show_plots': False,
         'save_plots': False,
         'save_folder': './',
-        'window_length': 3,
+        'interactive': False,
-        'polyorder': 2,
+        'smooth_window_length': 3,
-        'save_default': False
+        'smooth_polyorder': 2,
+        'smooth_algorithm': 'savgol', # At the present, only Savitzky-Golay filter is implemented. Add Gaussian and Boxcar later.
+        'smooth_save_default': False,
+        'smooth_store_data': False,
     }
     options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
 
     df_smooth = pd.DataFrame(data['xanes_data']['ZapEnergy'])
 
-    if options['save_default']:
+    if options['smooth_save_default']:
         df_smooth_default = pd.DataFrame(data['xanes_data']['ZapEnergy'])
 
+    if options['log']:
+        aux.write_log(message='Starting smoothing.')
+
+
+    if options['interactive']:
+        data['xanes_data_backup'] = data['xanes_data']
+        options['interactive'] = False
+        options['interactive_session_active'] = True
+        options['show_plots'] = True
+        smoothing_interactive(data=data, options=options)
+        return
+
+
     # 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 i, filename in enumerate(data['path']):
-        df_smooth.insert(1, filename, savgol_filter(data['xanes_data'][filename], options['window_length'], options['polyorder']))
 
-        if options['save_default']:
+        if options['smooth_algorithm'] == 'savgol':
-            df_smooth_default.insert(1, filename, savgol_filter(data['xanes_data'][filename], default_options['window_length'], default_options['polyorder']))
+            if options['log']:
+                aux.write_log(message=f'Smoothing {filename} with algorithm: {options["smooth_algorithm"]} ({i+1}/{len(data["path"])})', options=options)
+            df_smooth.insert(1, filename, savgol_filter(data['xanes_data'][filename], options['smooth_window_length'], options['smooth_polyorder']))
         
+        if options['smooth_save_default']:
+            if options['smooth_algorithm'] == 'savgol':
+                if options['log']:
+                    aux.write_log(message=f'Smoothing {filename} using default parameters with algorithm: {options["smooth_algorithm"]} ({i+1}/{len(data["path"])})', options=options)
+                df_smooth_default.insert(1, filename, savgol_filter(data['xanes_data'][filename], default_options['smooth_window_length'], default_options['smooth_polyorder']))
+        
+
+        if options['save_plots'] or options['show_plots']:
+
+            
+
+            edge_pos = estimate_edge_position(data=data, options=options)
+            intensity_midpoint = df_smooth[filename].iloc[np.where(df_smooth['ZapEnergy'] == find_nearest(df_smooth['ZapEnergy'], edge_pos))].values[0]
+            step_length = data['xanes_data']['ZapEnergy'].iloc[1] - data['xanes_data']['ZapEnergy'].iloc[0]
+
+
+    
+            if options['smooth_save_default']:
+                fig, (ax1, ax2) = plt.subplots(1,2,figsize=(20,5))
+                data['xanes_data'].loc[(data['xanes_data']['ZapEnergy'] > edge_pos-10*step_length) & (data['xanes_data']['ZapEnergy'] < edge_pos+10*step_length)].plot(x='ZapEnergy', y=filename, color='black', ax=ax1, kind='scatter')
+                df_smooth.loc[(df_smooth['ZapEnergy'] > edge_pos-10*step_length) & (df_smooth['ZapEnergy'] < edge_pos+10*step_length)].plot(x='ZapEnergy', y=filename, color='red', ax=ax1)
+                ax1.set_title(f'{os.path.basename(filename)} - Smooth', size=20)
+
+                data['xanes_data'].loc[(data['xanes_data']['ZapEnergy'] > edge_pos-10*step_length) & (data['xanes_data']['ZapEnergy'] < edge_pos+10*step_length)].plot(x='ZapEnergy', y=filename, color='black', ax=ax2,  kind='scatter')
+                df_smooth_default.loc[(df_smooth_default['ZapEnergy'] > edge_pos-10*step_length) & (df_smooth_default['ZapEnergy'] < edge_pos+10*step_length)].plot(x='ZapEnergy', y=filename, color='red', ax=ax2)
+                ax2.set_title(f'{os.path.basename(filename)} - Smooth (default values)', size=20)
+
+            elif not options['smooth_save_default']:
+                fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(20,10))
+                data['xanes_data'].plot(x='ZapEnergy', y=filename, ax=ax1, kind='scatter', c='black')
+                df_smooth.plot(x='ZapEnergy', y=filename, ax=ax1, c='red')
+
+                data['xanes_data'].loc[(data['xanes_data']['ZapEnergy'] > edge_pos-10*step_length) & (data['xanes_data']['ZapEnergy'] < edge_pos+10*step_length)].plot(x='ZapEnergy', y=filename, color='black', ax=ax2,  kind='scatter')
+                df_smooth.loc[(df_smooth['ZapEnergy'] > edge_pos-10*step_length) & (df_smooth['ZapEnergy'] < edge_pos+10*step_length)].plot(x='ZapEnergy', y=filename, color='red', ax=ax2)
+                #ax.set_xlim([edge_pos-0.0015, edge_pos+0.0015])
+                #ax.set_ylim([intensity_midpoint*0.9, intensity_midpoint*1.1])
+                
+                ax1.set_title(f'{os.path.basename(filename)} - Smooth', size=20)
+                ax2.set_title(f'{os.path.basename(filename)} - Smooth Edge Region', size=20)
 
             if options['save_plots']:
                 if not os.path.isdir(options['save_folder']):
                     os.makedirs(options['save_folder'])
 
                 dst = os.path.join(options['save_folder'], os.path.basename(filename)) + '_smooth.png'
-
-            edge_pos = estimate_edge_position(data=data, options=options)
-            intensity_midpoint = df_smooth[filename].iloc[np.where(df_smooth['ZapEnergy'] == find_nearest(df_smooth['ZapEnergy'], edge_pos))].values[0]
-    
-            if options['save_default']:
-                fig, (ax1, ax2) = plt.subplots(1,2,figsize=(20,5))
-                data['xanes_data'].loc[(data['xanes_data']['ZapEnergy'] > edge_pos-0.0015) & (data['xanes_data']['ZapEnergy'] < edge_pos+0.0015)].plot(x='ZapEnergy', y=filename, color='black', ax=ax1, kind='scatter')
-                df_smooth.loc[(df_smooth['ZapEnergy'] > edge_pos-0.0015) & (df_smooth['ZapEnergy'] < edge_pos+0.0015)].plot(x='ZapEnergy', y=filename, color='red', ax=ax1)
-                ax1.set_title(f'{os.path.basename(filename)} - Smooth', size=20)
-
-                data['xanes_data'].loc[(data['xanes_data']['ZapEnergy'] > edge_pos-0.0015) & (data['xanes_data']['ZapEnergy'] < edge_pos+0.0015)].plot(x='ZapEnergy', y=filename, color='black', ax=ax2,  kind='scatter')
-                df_smooth_default.loc[(df_smooth_default['ZapEnergy'] > edge_pos-0.0015) & (df_smooth_default['ZapEnergy'] < edge_pos+0.0015)].plot(x='ZapEnergy', y=filename, color='red', ax=ax2)
-                ax2.set_title(f'{os.path.basename(filename)} - Smooth (default values)', size=20)
-
-            elif not options['save_default']:
-                fig, ax = plt.subplots(figsize=(10,5))
-                data['xanes_data'].loc[(data['xanes_data']['ZapEnergy'] > edge_pos-0.0015) & (data['xanes_data']['ZapEnergy'] < edge_pos+0.0015)].plot(x='ZapEnergy', y=filename, color='black', ax=ax,  kind='scatter')
-                df_smooth.loc[(df_smooth['ZapEnergy'] > edge_pos-0.0015) & (df_smooth['ZapEnergy'] < edge_pos+0.0015)].plot(x='ZapEnergy', y=filename, color='red', ax=ax)
-                ax.set_xlim([edge_pos-0.0015, edge_pos+0.0015])
-                ax.set_ylim([intensity_midpoint*0.9, intensity_midpoint*1.1])
-                
-                ax.set_title(f'{os.path.basename(filename)} - Smooth', size=20)
-
-
                 plt.savefig(dst, transparent=False)
+            
+            if not options['show_plots']:
                 plt.close()
     
-    if not options['save_default']:
+    if not options['smooth_save_default']:
         df_smooth_default = None
 
+    if options['smooth_store_data']:
+        data['xanes_data'] = df_smooth
+        options['smooth_store_data'] = False
+    
     return df_smooth, df_smooth_default
 
 
 
+def smoothing_interactive(data: dict, options: dict) -> None:
+    ''' Defines the widgets to use with the ipywidgets interactive mode and calls the update function found in btp.ipywidgets. '''
+
+    w = widgets.interactive(
+        btp.ipywidgets_update, func=widgets.fixed(smoothing), data=widgets.fixed(data), options=widgets.fixed(options), 
+        smooth_window_length=widgets.IntSlider(value=options['smooth_window_length'], min=3, max=21, step=2),
+        smooth_polyorder=widgets.IntSlider(value=options['smooth_polyorder'],  min=1, max=5, step=1),
+        smooth_store_data=widgets.Checkbox(value=options['smooth_store_data'])
+    )
+    
+    options['widget'] = w
+
+    display(w)
+
+
+def restore_from_backup(data):
+    if 'xanes_data_bakcup' in data.keys():
+        data['xanes_data'] = data['xanes_data_backup']
+
+
 def find_nearest(array, value):
     #function to find the value closes to "value" in an "array"
     array = np.asarray(array)
@@ -327,7 +515,7 @@ def estimate_edge_position(data: dict, options={}, index=0):
     default_options = {
         'log': False,
         'logfile': f'{datetime.now().strftime("%Y-%m-%d-%H-%M-%S")}_edge_position_estimation.log',
-        'periods': 2, #Periods needs to be an even number for the shifting of values to work properly
+        'periods': 6, #Periods needs to be an even number for the shifting of values to work properly
     }
     options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
 
@@ -348,52 +536,85 @@ def estimate_edge_position(data: dict, options={}, index=0):
     return estimated_edge_shift
 
 def determine_edge_position(data: dict, options={}):
+    ''' Determines the edge position by 1) first differential maximum and/or 2) second differential zero-point. Calculates differential and/or double differential by diff.periods and double_diff.periods respectively.
+    The differentiated and/or doubly differentiated data is fitted to a polynomial of diff.polyorder and/or double_diff.polyorder around the estimated edge position. The estimated edge position is set to be the x-value of the data 
+    point at maximum of the differentiated data. The region to be fitted to the polynomial is determined by fit_region, which defaults to 5 times the distance between two data points, giving five data points to fit to.
     
-    required_options = ['save_values', 'log', 'logfile', 'save_plots', 'save_folder', 'periods', 'diff', 'double_diff', 'fit_region']
+    Allows plotting and saving of three plots to assess the quality of the fit, and also allows logging.
+    
+    Requires that XANES-data is already loaded in data['xanes_data']. This allows the user to choose when to determine the edge position - whether before or after normalisation, flattening etc.'''
+    
+    required_options = ['save_values', 'log', 'logfile', 'show_plots', 'save_plots', 'save_folder',  'diff', 'diff.polyorder', 'diff.periods', 'double_diff', 'double_diff.polyorder', 'double_diff.periods', 'points_around_edge']
     default_options = {
-        'save_values': True,
+        'save_values': True, # Whether the edge positions should be stored in a dictionary within the main data dictionary. 
-        'log': False,
+        'log': False, # Toggles logging on/off
-        'logfile': f'{datetime.now().strftime("%Y-%m-%d-%H-%M-%S")}_determine_edge_position.log',
+        'logfile': f'{datetime.now().strftime("%Y-%m-%d-%H-%M-%S")}_determine_edge_position.log', # Sets the path to the logfile. Ignored if log == False
-        'save_plots': False,
+        'show_plots': False, #  Toggles on/off whether plots should be shown. For sequential data, saving the plots and inspecting them there is probably better.
-        'save_folder': './',
+        'save_plots': False, # Toggles on/off whether plots should be saved. 
-        'periods': 2, #Periods needs to be an even number for the shifting of values to work properly,
+        'save_folder': './', # Sets the path to where the plots should be saved. Creates folder if doesn't exist. Ignored if save_plots == False
-        'diff': True,
+        'diff': True, # Toggles calculation of the edge position based on differential data
-        'double_diff': False,
+        'diff.polyorder': 2, # Sets the order of the polynomial to fit edge region of the differential to
-        'fit_region': 0.0005
+        'diff.periods': 2, # Sets the number of data points between which the first order difference should be calculated. Needs to be even for subsequent shifting of data to function.
-    
+        'double_diff': False, # Toggles calculation of the edge position based on double differential data
+        'double_diff.polyorder': 1, # Sets the order of the polynomial to fit edge region of the double differential to
+        'double_diff.periods': 2, # Sets the number of data points between which the second order difference should be calculated. Needs to be even for subsequent shifting of data to function.
+        'points_around_edge': 5 # The length of the region to find points to fit to a function
     }
 
     options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
 
-    if options['periods'] % 2 == 1:
+
+    # Check if periods are even
+    if options['diff'] and options['diff.periods'] % 2 != 0:
+        if options['log']:
+            aux.write_log(message='Periods for differentiation is not even. Ending run.', options=options)
+        raise Exception("NB! Periods needs to be an even number for the shifting of values to work properly")
+    if options['double_diff'] and options['double_diff.periods'] % 2 != 0:
+        aux.write_log(message='Periods for double differentiation is not even. Ending run.', options=options)
         raise Exception("NB! Periods needs to be an even number for the shifting of values to work properly")
 
 
-    #####
+    if options['interactive']:
+        data['xanes_data_backup'] = data['xanes_data']
+        options['interactive'] = False
+        options['interactive_session_active'] = True
+        options['show_plots'] = True
+        determine_edge_position_interactive(data=data, options=options)
+        return
 
+
+   
+    
+    # Prepare dataframes for differential data
     if options['diff']:
         df_diff = pd.DataFrame(data['xanes_data']['ZapEnergy'])
     if options['double_diff']:
         df_double_diff = pd.DataFrame(data['xanes_data']['ZapEnergy'])
     if options['save_values']:
-        data['e0'] = {}
+        data['e0_diff'] = {}
+        data['e0_double_diff'] = {}
 
 
+    # Get rough estimate of edge position
     for i, filename in enumerate(data['path']):
         estimated_edge_pos = estimate_edge_position(data, options=options, index=i)
 
         
-        #========================== fitting first differential ==========
+        fit_region = (options['points_around_edge']+1)*(data['xanes_data']['ZapEnergy'].iloc[1] - data['xanes_data']['ZapEnergy'].iloc[0])
+
+
+        #========================== Fitting the first order derivative ==========
 
         if options['diff']:
-            df_diff[filename] = data['xanes_data'][filename].diff(periods=options['periods'])
+            df_diff[filename] = data['xanes_data'][filename].diff(periods=options['diff.periods']) 
-            df_diff[filename]=df_diff[filename].shift(-int(options['periods']/2))
+            df_diff[filename]=df_diff[filename].shift(-int(options['diff.periods']/2)) # Shifts the data back so that the difference between the points is located in the middle of the two points the caluclated difference is between
 
-            df_diff_edge = df_diff.loc[(df_diff["ZapEnergy"] < estimated_edge_pos+options['fit_region']) & ((df_diff["ZapEnergy"] > estimated_edge_pos-options['fit_region']))]
+            # Picks out the points to be fitted
+            df_diff_edge = df_diff.loc[(df_diff["ZapEnergy"] <= estimated_edge_pos+fit_region) & ((df_diff["ZapEnergy"] >= estimated_edge_pos-fit_region))]
     
             
             # Fitting a function to the chosen interval
-            params = np.polyfit(df_diff_edge["ZapEnergy"], df_diff_edge[filename], 2)
+            params = np.polyfit(df_diff_edge["ZapEnergy"], df_diff_edge[filename], options['diff.polyorder'])
             diff_function = np.poly1d(params)
 
             x_diff=np.linspace(df_diff_edge["ZapEnergy"].iloc[0],df_diff_edge["ZapEnergy"].iloc[-1],num=10000)
@@ -407,21 +628,21 @@ def determine_edge_position(data: dict, options={}):
             edge_pos_diff=x_diff[np.where(y_diff == np.amax(y_diff))][0]
             
             if options['log']:
-                aux.write_log(message=f"Edge position estimated by the differential maximum is: {str(round(edge_pos_diff,5))}", options=options)
+                aux.write_log(message=f"Edge position estimated by the differential maximum is: {str(round(edge_pos_diff,5))} keV", options=options)
             
             if options['save_values']:
-                data['e0'][filename] = edge_pos_diff
+                data['e0_diff'][filename] = edge_pos_diff
-
 
+         #========================== Fitting the second order derivative ==========
         if options['double_diff']:
-            df_double_diff[filename] = data['xanes_data'][filename].diff(periods=options['periods']).diff(periods=options['periods'])
+            df_double_diff[filename] = data['xanes_data'][filename].diff(periods=options['double_diff.periods']).diff(periods=options['double_diff.periods'])
-            df_double_diff[filename]=df_double_diff[filename].shift(-int(options['periods']))
+            df_double_diff[filename]=df_double_diff[filename].shift(-int(options['double_diff.periods']))
             
             # Pick out region of interest
-            df_double_diff_edge = df_double_diff.loc[(df_double_diff["ZapEnergy"] < estimated_edge_pos+options['fit_region']) & ((df_double_diff["ZapEnergy"] > estimated_edge_pos-options['fit_region']))]
+            df_double_diff_edge = df_double_diff.loc[(df_double_diff["ZapEnergy"] < estimated_edge_pos+fit_region) & ((df_double_diff["ZapEnergy"] > estimated_edge_pos-fit_region))]
 
             # Fitting a function to the chosen interval
-            params = np.polyfit(df_double_diff_edge["ZapEnergy"], df_double_diff_edge[filename], 2)
+            params = np.polyfit(df_double_diff_edge["ZapEnergy"], df_double_diff_edge[filename], options['double_diff.polyorder'])
             double_diff_function = np.poly1d(params)
 
             x_double_diff=np.linspace(df_double_diff_edge["ZapEnergy"].iloc[0], df_double_diff_edge["ZapEnergy"].iloc[-1],num=10000)
@@ -436,67 +657,109 @@ def determine_edge_position(data: dict, options={}):
             edge_pos_double_diff=x_double_diff[np.where(y_double_diff == find_nearest(y_double_diff,0))][0]
         
             if options['log']:
-                aux.write_log(message=f"Edge shift estimated by the double differential zero-point is {str(round(edge_pos_double_diff,5))}", options=options)
+                aux.write_log(message=f"Edge position estimated by the double differential zero-point is {str(round(edge_pos_double_diff,5))} keV", options=options)
 
-            if options['save_plots']:
+                if options['diff']:
+                    aux.write_log(message=f"Difference between edge position estimated from differential maximum and double differential zero-point is {(edge_pos_diff-edge_pos_double_diff)*1000} eV.")
 
+            if options['save_values']:
+                data['e0_double_diff'][filename] = edge_pos_double_diff
+
+
+        # Make and show / save plots
+        if options['save_plots'] or options['show_plots']:
+
+
+            # If both are enabled
             if options['diff'] and options['double_diff']:
 
-                    fig, ((ax1, ax2), (ax3, ax4)) = plt.subplots(ncols=2, nrows=2, figsize=(20,20))
+                fig, ((ax1, ax2, ax3), (ax4, ax5, ax6)) = plt.subplots(ncols=3, nrows=2, figsize=(20,20))
-                    df_diff.plot(x='ZapEnergy', y=filename, ax=ax1, kind='scatter')
+                data['xanes_data'].plot(x='ZapEnergy', y=filename, ax=ax1, c='black')
-                    df_diff_fit_function.plot(x='x_diff', y='y_diff', ax=ax1)
-                    ax1.set_xlim([edge_pos_diff-0.0015, edge_pos_diff+0.0015])
-                    ax1.axvline(x=edge_pos_diff-options['fit_region'], ls='--', c='black')
                 ax1.axvline(x=edge_pos_diff, ls='--', c='green')
-                    ax1.axvline(x=edge_pos_diff+options['fit_region'], ls='--', c='black')
-                    ax1.set_title('Fit region of differentiated data')
                 
-                    df_diff_edge.plot(x='ZapEnergy', y=filename, ax=ax2, kind='scatter')
+                df_diff.plot(x='ZapEnergy', y=filename, ax=ax2, kind='scatter')
                 df_diff_fit_function.plot(x='x_diff', y='y_diff', ax=ax2)
+                ax2.set_xlim([edge_pos_diff-fit_region*1.5, edge_pos_diff+fit_region*1.5])
+                ax2.axvline(x=estimated_edge_pos-fit_region, ls='--', c='black')
                 ax2.axvline(x=edge_pos_diff, ls='--', c='green')
-                    ax2.axvline(x=estimated_edge_pos, ls='--', c='red')
+                ax2.axvline(x=estimated_edge_pos+fit_region, ls='--', c='black')
-                    ax2.set_title('Fit of differentiated data')
+                ax2.set_title('Fit region of differentiated data')
+
+                df_diff_edge.plot(x='ZapEnergy', y=filename, ax=ax3, kind='scatter')
+                df_diff_fit_function.plot(x='x_diff', y='y_diff', ax=ax3)
+                ax3.axvline(x=edge_pos_diff, ls='--', c='green')
+                ax3.axvline(x=estimated_edge_pos, ls='--', c='red')
+                ax3.set_title('Fit of differentiated data')
 
 
-                    df_double_diff.plot(x='ZapEnergy', y=filename, ax=ax3, kind='scatter')
+                data['xanes_data'].plot(x='ZapEnergy', y=filename, ax=ax4, c='black')
-                    df_double_diff_fit_function.plot(x='x_diff', y='y_diff', ax=ax3)
-                    ax3.set_xlim([edge_pos_double_diff-0.0015, edge_pos_double_diff+0.0015])
-                    ax3.axvline(x=edge_pos_double_diff-options['fit_region'], ls='--', c='black')
-                    ax3.axvline(x=edge_pos_double_diff, ls='--', c='green')
-                    ax3.axvline(x=edge_pos_double_diff+options['fit_region'], ls='--', c='black')
-
-                    df_double_diff_edge.plot(x='ZapEnergy', y=filename, ax=ax4, kind='scatter')
-                    df_double_diff_fit_function.plot(x='x_diff', y='y_diff', ax=ax4)
                 ax4.axvline(x=edge_pos_double_diff, ls='--', c='green')
-                    ax4.axvline(x=estimated_edge_pos, ls='--', c='red')
+
-
+                df_double_diff.plot(x='ZapEnergy', y=filename, ax=ax5, kind='scatter')
-                    
+                df_double_diff_fit_function.plot(x='x_diff', y='y_diff', ax=ax5)
+                ax5.set_xlim([edge_pos_double_diff-0.0015, edge_pos_double_diff+0.0015])
+                ax5.axvline(x=estimated_edge_pos-fit_region, ls='--', c='black')
+                ax5.axvline(x=edge_pos_double_diff, ls='--', c='green')
+                ax5.axvline(x=estimated_edge_pos+fit_region, ls='--', c='black')
+
+                df_double_diff_edge.plot(x='ZapEnergy', y=filename, ax=ax6, kind='scatter')
+                df_double_diff_fit_function.plot(x='x_diff', y='y_diff', ax=ax6)
+                ax6.axvline(x=edge_pos_double_diff, ls='--', c='green')
+                ax6.axvline(x=estimated_edge_pos, ls='--', c='red')
                 
 
+            # If only first order differentials is enabled
             elif options['diff']:
-                    fig, (ax1, ax2) = plt.subplots(ncols=2,nrows=1, figsize=(20, 10))
+                fig, (ax1, ax2, ax3) = plt.subplots(ncols=3,nrows=1, figsize=(20, 10))
-                    df_diff.plot(x='ZapEnergy', y=filename, ax=ax1, kind='scatter')
+                
-                    ax1.set_xlim([edge_pos_diff-0.5, edge_pos_diff+0.5])
+                data['xanes_data'].plot(x='ZapEnergy', y=filename, ax=ax1, c='black')
-                    ax1.axvline(x=edge_pos_diff-options['fit_region'], ls='--', c='black')
                 ax1.axvline(x=edge_pos_diff, ls='--', c='green')
-                    ax1.axvline(x=edge_pos_diff+options['fit_region'], ls='--', c='black')
 
-                    df_diff_edge.plot(x='ZapEnergy', y=filename, ax=ax2)
+                df_diff.plot(x='ZapEnergy', y=filename, ax=ax2, kind='scatter')
+                df_diff_fit_function.plot(x='x_diff', y='y_diff', ax=ax2)
+                ax2.set_xlim([edge_pos_diff-fit_region*1.5, edge_pos_diff+fit_region*1.5])
+                ax2.axvline(x=edge_pos_diff-fit_region, ls='--', c='black')
                 ax2.axvline(x=edge_pos_diff, ls='--', c='green')
-                    ax2.axvline(x=estimated_edge_pos, ls='--', c='red')
+                ax2.axvline(x=edge_pos_diff+fit_region, ls='--', c='black')
 
+                df_diff_edge.plot(x='ZapEnergy', y=filename, ax=ax3)
+                df_diff_fit_function.plot(x='x_diff', y='y_diff', ax=ax3)
+                ax3.axvline(x=edge_pos_diff, ls='--', c='green')
+                ax3.axvline(x=estimated_edge_pos, ls='--', c='red')
 
+            # If only second order differentials is enabled
             elif options['double_diff']:
-                    fig, (ax1, ax2) = plt.subplots(ncols=2,nrows=1, figsize=(20, 10))
+                fig, (ax1, ax2, ax3) = plt.subplots(ncols=3,nrows=1, figsize=(20, 10))
-                    df_double_diff.plot(x='ZapEnergy', y=filename, ax=ax1, kind='scatter')
-                    ax1.set_xlim([edge_pos_double_diff-0.5, edge_pos_double_diff+0.5])
-                    ax1.axvline(x=edge_pos_double_diff-options['fit_region'], ls='--', c='black')
-                    ax1.axvline(x=edge_pos_double_diff, ls='--', c='green')
-                    ax1.axvline(x=edge_pos_double_diff+options['fit_region'], ls='--', c='black')
                 
-                    df_double_diff_edge.plot(x='ZapEnergy', y=filename, ax=ax2)
+                data['xanes_data'].plot(x='ZapEnergy', y=filename, ax=ax1, c='black')
+                ax1.axvline(x=edge_pos_double_diff, ls='--', c='green')
+
+                df_double_diff.plot(x='ZapEnergy', y=filename, ax=ax2, kind='scatter')
+                df_double_diff_fit_function.plot(x='x_diff', y='y_diff', ax=ax2)
+                ax2.set_xlim([edge_pos_double_diff-fit_region*1.5, edge_pos_double_diff+fit_region*1.5])
+                ax2.axvline(x=edge_pos_double_diff-fit_region, ls='--', c='black')
                 ax2.axvline(x=edge_pos_double_diff, ls='--', c='green')
-                    ax2.axvline(x=estimated_edge_pos, ls='--', c='red')
+                ax2.axvline(x=edge_pos_double_diff+fit_region, ls='--', c='black')
+
+                df_double_diff_edge.plot(x='ZapEnergy', y=filename, ax=ax3)
+                df_double_diff_fit_function.plot(x='x_diff', y='y_diff', ax=ax3)
+                ax3.axvline(x=edge_pos_double_diff, ls='--', c='green')
+                ax3.axvline(x=estimated_edge_pos, ls='--', c='red')
+
+
+            # Save plots if toggled
+            if options['save_plots']:
+                if not os.path.isdir(options['save_folder']):
+                    os.makedirs(options['save_folder'])
+
+                dst = os.path.join(options['save_folder'], os.path.basename(filename)) + '_edge_position.png'
+
+                plt.savefig(dst, transparent=False)
+
+
+            # Close plots if show_plots not toggled
+            if not options['show_plots']:
+                plt.close()
 
 
     if not options['diff']:
@@ -506,35 +769,59 @@ def determine_edge_position(data: dict, options={}):
 
     return edge_pos_diff, edge_pos_double_diff
 
+
+
+def determine_edge_position_interactive(data: dict, options: dict) -> None:
+    ''' Defines the widgets to use with the ipywidgets interactive mode and calls the update function found in btp.ipywidgets. '''
+
+
+    step_size = data['xanes_data']['ZapEnergy'].iloc[1] - data['xanes_data']['ZapEnergy'].iloc[0]
+
+    w = widgets.interactive(
+        btp.ipywidgets_update, func=widgets.fixed(determine_edge_position), data=widgets.fixed(data), options=widgets.fixed(options), 
+        points_around_edge=widgets.IntSlider(value=options['points_around_edge'], min=1, max=20, step=1),   
+    )
+    
+    options['widget'] = w
+
+    display(w)
+
 def normalise(data: dict, options={}):
-    required_options = ['log', 'logfile', 'save_values']
+    required_options = ['log', 'logfile', 'normalisation_store_data']
     default_options = {
         'log': False,
         'logfile': f'{datetime.now().strftime("%Y-%m-%d-%H-%M-%S")}_normalisation.log',
-        'save_values': True
+        'normalisation_store_data': False,
     }
     options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
 
     normalised_df = pd.DataFrame(data['xanes_data']['ZapEnergy'])
     data['normalisation_constants'] = {}
+    if options['normalisation_store_data']:
+        pre_edge_fit_data_norm = pd.DataFrame(data['pre_edge_fit_data']['ZapEnergy'])
+        post_edge_fit_data_norm = pd.DataFrame(data['post_edge_fit_data']['ZapEnergy'])
 
     #Finding the normalisation constant µ_0(E_0), by subtracting the value of the pre-edge-line from the value of the post-edge line at e0
     for filename in data['path']:
-        e0_ind = data['post_edge_fit_data'].loc[data['post_edge_fit_data']['ZapEnergy'] == find_nearest(data['post_edge_fit_data']['ZapEnergy'], data['e0'][filename])].index.values[0]
+        e0_ind = data['post_edge_fit_data'].loc[data['post_edge_fit_data']['ZapEnergy'] == find_nearest(data['post_edge_fit_data']['ZapEnergy'], data['e0_diff'][filename])].index.values[0]
         #norm = data['post_edge_fit_data'][filename].iloc[find_nearest(data['post_edge_fit_data'][filename], data['e0'][filename])]
         normalisation_constant = data['post_edge_fit_data'][filename].iloc[e0_ind] - data['pre_edge_fit_data'][filename].iloc[e0_ind]
         normalised_df.insert(1, filename, data['xanes_data'][filename] / normalisation_constant)
 
+        if options['normalisation_store_data']:
+            pre_edge_fit_data_norm.insert(1, filename, data['pre_edge_fit_data'][filename] / normalisation_constant)
+            post_edge_fit_data_norm.insert(1, filename, data['post_edge_fit_data'][filename] / normalisation_constant)
 
+
+
+    if options['normalisation_store_data']:
+        data['xanes_data'] = normalised_df
         # Normalise the pre-edge and post-edge fit function data
-        data['pre_edge_fit_data'][filename] = data['pre_edge_fit_data'][filename] / normalisation_constant
+        data['pre_edge_fit_data_norm'] = pre_edge_fit_data_norm
-        data['post_edge_fit_data'][filename] = data['post_edge_fit_data'][filename] / normalisation_constant
+        data['post_edge_fit_data_norm'] = post_edge_fit_data_norm
 
         data['normalisation_constants'][filename] = normalisation_constant
 
-    if options['save_values']:
-        data['xanes_data'] = normalised_df
-
 
     return normalised_df
 
@@ -542,11 +829,11 @@ def normalise(data: dict, options={}):
 def flatten(data:dict, options={}):
     #only picking out zapenergy-values higher than edge position (edge pos and below remains untouched)
 
-    required_options = ['log', 'logfile', 'save_values']
+    required_options = ['log', 'logfile', 'flatten_store_data']
     default_options = {
         'log': False,
         'logfile': f'{datetime.now().strftime("%Y-%m-%d-%H-%M-%S")}_flattening.log',
-        'save_values': True
+        'flatten_store_data': False,
     }
     options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
 
@@ -554,13 +841,14 @@ def flatten(data:dict, options={}):
     flattened_df = pd.DataFrame(data['xanes_data']['ZapEnergy'])
 
     for filename in data['path']:
-        fit_function_diff = -data['post_edge_fit_data'][filename] + data['pre_edge_params'][filename][0]
+        fit_function_diff = data['post_edge_fit_data_norm'][filename] - 1
-        fit_function_diff.loc[flattened_df['ZapEnergy'] <= data['e0'][filename]] = 0
+        
+        fit_function_diff.loc[flattened_df['ZapEnergy'] <= data['e0_diff'][filename]] = 0
 
         flattened_df[filename] = data['xanes_data'][filename] - fit_function_diff
 
 
-    if options['save_values']:
+    if options['flatten_store_data']:
         data['xanes_data'] = flattened_df
     
 

nafuma/xanes/edges.py

@@ -0,0 +1,30 @@
+import pandas as pd
+import numpy as np
+from scipy.constants import c, h
+
+# From 2019 redefinition of SI base units: https://en.wikipedia.org/wiki/2019_redefinition_of_the_SI_base_units
+keV_per_J = (1 / 1.602176634e-19) / 1000
+
+# kXu values taken from International Tables for Crystallography Volume , Kulwer Academic Publishers - Dordrect / Boston / London (1992)
+K = {   'Z':    [ 1, 2,
+                        3, 4, 5, 6, 7, 8, 9, 10,
+                        11, 12, 13, 14, 15, 16, 17, 18,
+                        19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36,
+                        37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48], 
+            'Atom': [   'H', 'He',
+                        'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne',
+                        'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar',
+                        'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr',
+                        'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd'], 
+            'kXu': [    np.nan, np.nan,
+                        226.5, np.nan, np.nan, 43.68, 30.99, 23.32, np.nan, np.nan, 
+                        np.nan, 9.5117, 7.9511, 6.7446, 5.7866, 5.0182, 4.3969, 3.8707, 
+                        3.43645, 3.07016, 2.7573, 2.49730, 2.26902, 2.07012, 1.89636, 1.74334, 1.60811, 1.48802, 1.38043, 1.2833, 1.19567, 1.11652, 1.04497, 0.97978, 0.91995, 0.86547,
+                        0.81549, 0.76969, 0.72762, 0.68877, 0.65291, 0.61977, 0.5891, 0.56047, 0.53378, 0.50915, 0.48582, 0.46409]}
+
+
+K = pd.DataFrame(K)
+K['keV'] = np.round(h*c/(K['kXu']*10**-10) * keV_per_J, 3)
+
+
+# FIXME If needed, add energies for L-edges as well.