Merge pull request #13 from rasmusthog/rasmus_xanes

Merge new XANES-functionality into main

nafuma/xanes/__init__.py

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

nafuma/xanes/calib.py

@@ -462,8 +462,6 @@ def smoothing(data: dict, options={}):
         # Make plots ...
         if options['save_plots'] or options['show_plots']:
 
-            
-
             edge_pos = estimate_edge_position(data=data, options=options)
             step_length = data['xanes_data']['ZapEnergy'].iloc[1] - data['xanes_data']['ZapEnergy'].iloc[0]
 
@@ -563,8 +561,8 @@ def estimate_edge_position(data: dict, options={}, index=0):
     options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
 
     #making new dataframe to keep the differentiated data
-    df_diff = pd.DataFrame(data['xanes_data_original']["ZapEnergy"])
+    df_diff = pd.DataFrame(data['xanes_data']["ZapEnergy"])
-    df_diff[data['path'][index]]=data['xanes_data_original'][data['path'][index]].diff(periods=options['periods'])
+    df_diff[data['path'][index]]=data['xanes_data'][data['path'][index]].diff(periods=options['periods'])
 
     #shifting column values up so that average differential fits right between the points used in the calculation
     df_diff[data['path'][index]]=df_diff[data['path'][index]].shift(-int(options['periods']/2))

nafuma/xanes/io.py

@@ -82,10 +82,19 @@ def split_scan_data(data: dict, options={}) -> list:
 
         for i, scan_data in enumerate(scan_datas):
 
+            if 'ZapEnergy' not in headers[i]:
+                if options['log']:
+                    aux.write_log(message=f'... No valid scan data found... ({i+1}/{len(scan_datas)})', options=options)
+                continue
+                        
             xanes_df = pd.DataFrame(scan_data).apply(pd.to_numeric)
             xanes_df.columns = headers[i]
+
+            
             edge = find_element({'xanes_data_original': xanes_df})
         
+                
+
             if options['log']:
                 aux.write_log(message=f'... Starting data clean-up ({edge}-edge)... ({i+1}/{len(scan_datas)})', options=options)
 
@@ -183,15 +192,111 @@ def split_scan_data(data: dict, options={}) -> list:
 
 
 
+def save_data(data: dict, options={}) -> None:
+
+    required_options = ['save_folder', 'overwrite', 'log', 'logfile', 'filename']
+
+    default_options = {
+        'log': False,
+        'logfile': f'{datetime.datetime.now().strftime("%Y-%m-%d-%H-%M-%S")}_save_files.log',
+        'save_folder': 'saved_scans',
+        'overwrite': False,
+        'filename': f'{datetime.datetime.now().strftime("%Y-%m-%d-%H-%M-%S")}_exported_data.dat',
+        }
+
+    options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
+
+
+    # Check if there is any data to be saved
+    if not 'xanes_data' in data.keys():
+        if options['log']:
+             aux.write_log(message=f'There is not saved scan data in data. Exiting without saving...', options=options)
+
+        return None
+    
+    if not isinstance(data['xanes_data'], pd.DataFrame):
+        if options['log']:
+             aux.write_log(message=f'data["xanes_data"] has an invalid format. Exiting without saving...', options=options)
+
+        return None
+
+
+    # Make folder(s) if it/they do(es)n't exist
+    if not os.path.exists(options['save_folder']):
+        if options['log']:
+             aux.write_log(message=f'Destination folder does not exist. Creating folder...', options=options)
+
+        os.makedirs(options['save_folder'])
+
+
+
+    if os.path.exists(os.path.join('save_folder', options['filename'])):
+        if not options['overwrite']:
+            if options['log']:
+                aux.write_log(message=f'File already exists and overwrite disabled. Exiting without saving...', options=options)
+            return None
+        
+    with open(os.path.join(options['save_folder'], options['filename']), 'w') as f:
+
+        if 'e0_diff' in data.keys():
+            f.write(f'# Number of header lines: {len(data["path"])+1} \n')
+
+            for i, (path, e0) in enumerate(data['e0_diff'].items()):
+                f.write(f'# Scan_{i} \t {e0} \n')
+       
+        else:
+            f.write(f'# Number of header lines: {1}')
+        
+
+        data['xanes_data'].to_csv(f, sep='\t', index=False)
+
+
+    #data['xanes_data'].to_csv(os.path.join(options['save_folder'], options['filename']), sep='\t', index=False)
+
+
+
+def load_data(path: str) -> dict:
+    # FIXME Let this function be called by read_data() if some criterium is passed
+
+    data = {}
+
+
+    with open(path, 'r') as f:
+        line = f.readline()
+        header_lines = int(line.split()[-1])
+
+        if header_lines > 1:
+            edge_positions = []
+            line = f.readline()
+            while line[0] == '#':
+                edge_positions.append(line.split()[-1])
+                line = f.readline()
+
+    data['xanes_data'] = pd.read_csv(path, sep='\t', skiprows=header_lines)
+    data['path'] = data['xanes_data'].columns.to_list()
+    data['path'].remove('ZapEnergy')
+
+    if header_lines > 1:
+        data['e0_diff'] = {}
+
+        for path, edge_position in zip(data['path'], edge_positions):
+            data['e0_diff'][path] = float(edge_position)
+
+    
+
+    return data
+
+
 def read_data(data: dict, options={}) -> pd.DataFrame:
 
 
     # FIXME Handle the case when dataseries are not the same size
     # FIXME Add possibility to extract TIME (for operando runs) and Blower Temp (for variable temperature runs)
     # FIXME Add possibility to iport transmission data
-    required_options = ['adjust']
+    required_options = ['adjust', 'mode']
     default_options = {
-        'adjust': 0
+        'adjust': 0,
+        'mode': 'fluoresence'
     }
 
     options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
@@ -211,11 +316,15 @@ def read_data(data: dict, options={}) -> pd.DataFrame:
 
         scan_data = pd.read_csv(filename, skiprows=1)
 
+        if options['mode'] == 'fluoresence':
             if not options['active_roi']:
                 scan_data = scan_data[[determine_active_roi(scan_data)]]
             else:
                 scan_data = scan_data[options['active_roi']]
 
+        elif options['mode'] == 'transmission':
+            scan_data = scan_data['MonEx'] / scan_data['Ion2']
+
         xanes_data = pd.concat([xanes_data, scan_data], axis=1)
 
 

nafuma/xanes/plot.py

@@ -0,0 +1,164 @@
+import matplotlib.pyplot as plt
+from matplotlib.ticker import (MultipleLocator, FormatStrFormatter,AutoMinorLocator)
+
+import pandas as pd
+import numpy as np
+import math
+import datetime
+
+#import ipywidgets as widgets
+#from IPython.display import display
+
+import nafuma.xanes as xas
+import nafuma.plotting as btp
+import nafuma.auxillary	as aux
+
+
+def plot_xanes(data, options={}):
+
+
+	# Update options
+	required_options = ['which_scans', 'xlabel', 'ylabel', 'xunit', 'yunit', 'exclude_scans', 'colours', 'gradient', 'rc_params', 'format_params']	
+	default_options = {
+		'which_scans': 'all', 
+        'xlabel': 'Energy', 'ylabel': 'Intensity',
+        'xunit': 'keV', 'yunit': 'arb. u.',
+        'exclude_scans': [],
+		'colours': None, 
+		'gradient': False,
+		'rc_params': {},
+		'format_params': {}}
+
+	options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
+
+	
+	if not 'xanes_data' in data.keys():
+		data['xanes_data'] = xas.io.load_data(data=data, options=options)
+
+	# Update list of cycles to correct indices
+	update_scans_list(data=data, options=options)
+
+	colours = generate_colours(scans=options['which_scans'], options=options)
+
+	# Prepare plot, and read and process data
+	
+	fig, ax = btp.prepare_plot(options=options)
+
+
+	# Add counter to pick out correct colour
+	counter = 0
+	for i, path in enumerate(data['path']):
+		if i in options['which_scans']:
+			data['xanes_data'].plot(x='ZapEnergy', y=path, ax=ax, c=colours[counter])
+			counter += 1
+
+
+	fig, ax = btp.adjust_plot(fig=fig, ax=ax, options=options)
+
+	#if options['interactive_session_active']:
+	
+
+	return fig, ax 
+
+
+def pick_out_scans(metadata: dict, timestamp: list):
+
+	# If either start or end are None, set to way back when or way into the future
+	if not timestamp[0]:
+		timestamp[0] = datetime.datetime.strptime('1970 01 01 00:00:00', '%Y %m %d %H:%M:%S')
+	else:
+		timestamp[0] = datetime.datetime.strptime(timestamp[0], "%d.%b %y %H.%M.%S")
+	if not timestamp[1]:
+		timestamp[1] = datetime.datetime.strptime('3000 01 01 00:00:00', '%Y %m %d %H:%M:%S')
+	else:
+		timestamp[1] = datetime.datetime.strptime(timestamp[1], "%d.%b %y %H.%M.%S")
+
+	scans = []
+	for i, time in enumerate(metadata['time']):
+		if time >= timestamp[0] and time <= timestamp[1]:
+			scans.append(i)
+
+
+	return scans
+
+		
+
+
+
+
+def update_scans_list(data, options: dict) -> None:
+
+	if options['which_scans'] == 'all':
+		options['which_scans'] = [i for i in range(len(data['path']))]
+
+
+	elif isinstance(options['which_scans'], list):
+
+		scans =[]
+
+		for scan in options['which_scans']:
+			if isinstance(scan, int):
+				scans.append(scan-1)
+
+			elif isinstance(scan, tuple):
+				interval = [i-1 for i in range(scan[0], scan[1]+1)]
+				scans.extend(interval)
+
+		
+		options['which_scans'] = scans
+	
+	
+	# Tuple is used to define an interval - as elements tuples can't be assigned, I convert it to a list here.
+	elif isinstance(options['which_scans'], tuple):
+		which_scans = list(options['which_scans'])
+
+		if which_scans[0] <= 0:
+			which_scans[0] = 1
+
+		elif which_scans[1] < 0:
+			which_scans[1] = len(options['which_scans'])
+
+
+		options['which_scans'] = [i-1 for i in range(which_scans[0], which_scans[1]+1)]
+
+	
+	for i, scan in enumerate(options['which_scans']):
+		if scan in options['exclude_scans']:
+			del options['which_scans'][i]
+
+
+
+
+def generate_colours(scans, options):
+    # FIXME Make this a generalised function and use this instead of this and in the electrochemsitry submodule
+
+	# Assign colours from the options dictionary if it is defined, otherwise use standard colours.
+	if options['colours']:
+		colour = options['colours']
+	
+	else:
+		#colour =  (214/255, 143/255, 214/255) # Plum Web (#D68FD6), coolors.co
+		colour = (90/255, 42/255, 39/255) # Caput Mortuum(#5A2A27), coolors.co
+
+	# If gradient is enabled, find start and end points for each colour
+	if options['gradient']:
+
+		add = min([(1-x)*0.75 for x in colour])
+
+		colour_start = colour
+		colour_end = [x+add for x in colour]
+
+
+	# Generate lists of colours
+	colours = []
+	
+	for scan_number in range(0, len(scans)):
+		if options['gradient']:
+			weight_start = (len(scans) - scan_number)/len(scans)
+			weight_end = scan_number/len(scans)
+
+			colour = [weight_start*start_colour + weight_end*end_colour for start_colour, end_colour in zip(colour_start, colour_end)]
+			
+		colours.append(colour)
+
+	return colours