From e67846d6f27968186ccc20aaacbd124646e8aa2e Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Tue, 9 Aug 2022 16:41:53 +0200
Subject: [PATCH] Initial commit of plot_xanes

---
 nafuma/xanes/plot.py | 95 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 95 insertions(+)
 create mode 100644 nafuma/xanes/plot.py

diff --git a/nafuma/xanes/plot.py b/nafuma/xanes/plot.py
new file mode 100644
index 0000000..3341b9e
--- /dev/null
+++ b/nafuma/xanes/plot.py
@@ -0,0 +1,95 @@
+import matplotlib.pyplot as plt
+from matplotlib.ticker import (MultipleLocator, FormatStrFormatter,AutoMinorLocator)
+
+import pandas as pd
+import numpy as np
+import math
+
+#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=None):
+
+
+	# Update options
+	required_options = ['which_scans', 'colours', 'gradient', 'rc_params', 'format_params']	
+	default_options = {
+		'which_scans': 'all', 
+		'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(scans=data['path'], options=options)
+
+	colours = generate_colours(cycles=data['cycles'], options=options)
+
+	if options['interactive']:
+		options['interactive'], options['interactive_session_active'] = False, True
+		plot_gc_interactive(data=data, options=options)
+		return
+
+
+	# Prepare plot, and read and process data
+	
+	fig, ax = btp.prepare_plot(options=options)
+
+	for i, cycle in enumerate(data['cycles']):
+		if i in options['which_cycles']:
+			if options['charge']:
+				cycle[0].plot(x=options['x_vals'], y=options['y_vals'], ax=ax, c=colours[i][0])
+
+			if options['discharge']:
+				cycle[1].plot(x=options['x_vals'], y=options['y_vals'], ax=ax, c=colours[i][1])
+
+
+	if options['interactive_session_active']:
+		update_labels(options, force=True)
+	else:
+		update_labels(options)
+
+	fig, ax = btp.adjust_plot(fig=fig, ax=ax, options=options)
+
+	#if options['interactive_session_active']:
+	
+
+	return data['cycles'], fig, ax 
+
+
+
+
+
+def update_scans_list(scans, options: dict) -> None:
+
+	if options['which_scans'] == 'all':
+		options['which_scans'] = [i for i in range(len(scans))]
+
+
+	elif type(options['which_scans']) == list:
+		options['which_scans'] = [i-1 for i in options['which_scans']]
+	
+	
+	# Tuple is used to define an interval - as elements tuples can't be assigned, I convert it to a list here.
+	elif type(options['which_cycles']) == tuple:
+		which_cycles = list(options['which_cycles'])
+
+		if which_cycles[0] <= 0:
+			which_cycles[0] = 1
+
+		elif which_cycles[1] < 0:
+			which_cycles[1] = len(cycles)
+
+
+		options['which_cycles'] = [i-1 for i in range(which_cycles[0], which_cycles[1]+1)]
\ No newline at end of file