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

Initial func to make manual background data in inp

Browse source
This commit is contained in:
halvorhv 2022-10-14 17:09:42 +02:00
parent 366768ecbf
commit 82b0981ada
1 changed files with 48 additions and 2 deletions
Download patch file Download diff file Expand all files Collapse all files

48
nafuma/xrd/refinement.py
View file

@ -104,8 +104,53 @@ def make_initial_inp(data: dict, options={}):
fout.write(line)
def make_manual_background(data, options):
#FIXME generalize this so it works properly
#FIXME fix so that plotting is optional
import numpy as np
import nafuma.xrd as xrd
import matplotlib.pyplot as plt
default_options = {
'plot_background': True,
'interval_length': 0.05,
'save_dir': 'background'
}
if "noheaders" in data['path'][0]:
filename = os.path.basename(data['path'][0]).split('_noheaders.')[0]
else:
filename = os.path.basename(data['path'][0]).split('.')[0]
options = aux.update_options(options=options, default_options=default_options)
#data['background_in_q'] is a .txt-file with one column of x-values that are good starting points for background determination, as they should not include any peaks for that specific material
#importing the pre-made background points in Q into a dataframe
df_backgroundpoints_q=pd.read_csv(data['background_in_q'],names=["background_q"])
diffractogram, wavelength = xrd.io.read_xy(data=data)
#transferring q-range background to the respective wavelength
x_background_points=[]
for q in df_backgroundpoints_q["background_q"]:
twotheta=2*180/np.pi*np.arcsin(q*wavelength/(4*np.pi))
x_background_points.append(twotheta)
fig,ax=plt.subplots(figsize=(20,20))
diffractogram.plot(x="2th",y="I", kind="scatter",ax=ax)
intervallength=options['interval_length']
background=pd.DataFrame()
for i, x in enumerate(x_background_points):
test=diffractogram.loc[(diffractogram["2th"]>x-intervallength) & (diffractogram["2th"]<x+intervallength)]
background = pd.concat([background,test], ignore_index=True, sort=False)
background.plot(x="2th",y="I", ax=ax,color='red',kind="scatter")
fig2,ax2=plt.subplots(figsize=(20,10))
background.to_csv(os.path.join(options['save_dir'],filename+"_background.txt"),index=None, header=None,sep=' ')
def write_xdd(fout, data, options):
import nafuma.xrd as xrd
@ -138,10 +183,11 @@ def write_xdd(fout, data, options):
for i in range(options['background']):
fout.write('0 ')
#EXTRA for implementation of manual background:
if options['manual_background'] != False:
if options['manual_background']:
fout.write('\n\t\'manual background file:')
fout.write('\n\tuser_y my_shape {_xy #include "'+options['manual_background']+'"} \n')
fout.write('\tprm !my_scale = 1;: 1.00000')
fout.write('\tfit_obj !f_SR_pos1 = my_scale * (my_shape);')
# Write wavelength and LP-factor