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Add func for making general background in q

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This commit is contained in:
halvorhv 2022-10-19 17:06:15 +02:00
parent 82b0981ada
commit ecfe7106f1
1 changed files with 46 additions and 8 deletions
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48
nafuma/xrd/refinement.py
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@ -103,6 +103,31 @@ def make_initial_inp(data: dict, options={}):
for line in lines:
fout.write(line)
def make_general_background_in_q(data, options):
#Function where you get a txt.-file of q-values, based on the 2th values you have picked out manually from a data set. Idea is that the same background points can be used for several samples, measured at several wavelengths.
#The input is a list of 2th-values that the user has found by manually inspecting a data set
import numpy as np
import nafuma.xrd as xrd
import matplotlib.pyplot as plt
default_options = {
'save_dir': 'background',
'filename': 'test'
}
options = aux.update_options(options=options, default_options=default_options)
list_of_2th_values = data['2th_values']
#x_background_points=list_of_2th_values
x_background_points_q=[]
for x in list_of_2th_values:
q=np.abs((4*np.pi/data['wavelength'])*np.sin(x/2 * np.pi/180))
x_background_points_q.append(q)
background_points=pd.DataFrame(x_background_points_q)
background_filename="C:/Users/halvorhv/OneDriveUiO/1_OrderPaper/analysis/exsitu/probing_ordering/refinements/"+options['filename']+"_background_points_in_q.txt"
background_points.to_csv(background_filename,index=None, header=None)#,index=None, header=None,sep=' ')
def make_manual_background(data, options):
#FIXME generalize this so it works properly
@ -113,7 +138,7 @@ def make_manual_background(data, options):
default_options = {
'plot_background': True,
'interval_length': 0.05,
'interval_length': 0.05, #picking out the region to be fitted for each background point, bigger interval-length means a bigger region for each point.
'save_dir': 'background'
}
if "noheaders" in data['path'][0]:
@ -137,20 +162,33 @@ def make_manual_background(data, options):
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)
if options['plot_background']:
#Overview figure
fig,ax=plt.subplots(figsize=(20,10))
diffractogram.plot(x="2th",y="I", kind="scatter",ax=ax,title="Background points (red) plotted with "+filename)
background.plot(x="2th",y="I", ax=ax,color='red',kind="scatter")
fig2,ax2=plt.subplots(figsize=(20,10))
#Log-figure for closer inspection
diffractogram["I_log"]=np.log10(diffractogram["I"])
background["I_log"]=np.log10(background["I"])
background_logmax=max(background["I_log"])
background_logmin=min(background["I_log"])
background.to_csv(os.path.join(options['save_dir'],filename+"_background.txt"),index=None, header=None,sep=' ')
fig2,ax2=plt.subplots(figsize=(20,10))
diffractogram.plot(x="2th",y="I_log", kind="scatter",ax=ax2, title="Background ploints (red) plotted with "+filename+" (log)")
background.plot(x="2th",y="I_log", ax=ax2,color='red',kind="scatter")
ax2.set_ylim(background_logmin,background_logmax)
background[["2th","I"]].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