# -*- coding: utf-8 -*-
########### SVN repository information ###################
# $Date: 2023-05-11 18:08:12 -0500 (Thu, 11 May 2023) $
# $Author: toby $
# $Revision: 5577 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/imports/G2rfd_xye.py $
# $Id: G2rfd_xye.py 5577 2023-05-11 23:08:12Z toby $
########### SVN repository information ###################
'''
'''
from __future__ import division, print_function
import os.path as ospath
import numpy as np
import GSASIIobj as G2obj
import GSASIIpath
GSASIIpath.SetVersionNumber("$Revision: 5577 $")
npasind = lambda x: 180.*np.arcsin(x)/np.pi
npsind = lambda x: np.sin(np.pi*x/180.)
try: # fails on doc build
fourpi = 4.0*np.pi
_double_min = np.finfo(float).min
_double_max = np.finfo(float).max
except TypeError:
pass
[docs]
class txt_XRayReaderClass(G2obj.ImportReflectometryData):
'Routines to import X-ray q REFD data from a .xrfd or .xdat file'
def __init__(self):
super(self.__class__,self).__init__( # fancy way to self-reference
extensionlist=('.xrfd','.xdat'),
strictExtension=False,
formatName = 'q (A-1) step X-ray QRE data',
longFormatName = 'q (A-1) stepped X-ray text data file in Q,R,E order; E optional'
)
# Validate the contents -- make sure we only have valid lines
[docs]
def ContentsValidator(self, filename):
'Look through the file for expected types of lines in a valid q-step file'
fp = open(filename,'r')
Ndata = 0
for i,S in enumerate(fp):
if '#' in S[0]:
continue
vals = S.split()
if len(vals) >= 2:
try:
data = [float(val) for val in vals]
Ndata += 1
except ValueError:
pass
fp.close()
if not Ndata:
self.errors = 'No 2 or more column numeric data found'
return False
return True # no errors encountered
def Reader(self,filename, ParentFrame=None, **unused):
print ('Read a q-step text file')
x = []
y = []
w = []
sq = []
wave = 1.5428 #Cuka default
Temperature = 300
fp = open(filename,'r')
for i,S in enumerate(fp):
if len(S) == 1: #skip blank line
continue
if '=' in S:
self.comments.append(S[:-1])
if 'wave' in S.split('=')[0].lower():
try:
wave = float(S.split('=')[1])
except:
pass
continue
if '#' in S[0]:
continue
vals = S.split()
if len(vals) >= 2:
try:
data = [float(val) for val in vals]
x.append(float(data[0]))
f = float(data[1])
if f <= 0.0:
del x[-1]
continue
elif len(vals) > 2:
y.append(float(data[1]))
w.append(1.0/float(data[2])**2)
if len(vals) == 4:
sq.append(float(data[3]))
else:
sq.append(0.)
else:
y.append(float(data[1]))
w.append(1.0/(0.02*float(data[1]))**2)
sq.append(0.)
except ValueError:
msg = 'Error in line '+str(i+1)
print (msg)
continue
fp.close()
N = len(x)
for S in self.comments:
if 'Temp' in S.split('=')[0]:
try:
Temperature = float(S.split('=')[1])
except:
pass
self.instdict['wave'] = wave
self.instdict['type'] = 'RXC'
x = np.array(x)
self.reflectometrydata = [
x, # x-axis values q
np.array(y), # small angle pattern intensities
np.array(w), # 1/sig(intensity)^2 values (weights)
np.zeros(N), # calc. intensities (zero)
np.zeros(N), # obs-calc profiles
np.array(sq), # fix bkg
]
self.reflectometryentry[0] = filename
self.reflectometryentry[2] = 1 # xye file only has one bank
self.idstring = ospath.basename(filename)
# scan comments for temperature
self.Sample['Temperature'] = Temperature
return True
[docs]
class txt_NeutronReaderClass(G2obj.ImportReflectometryData):
'Routines to import neutron q REFD data from a .nrfd or .ndat file'
def __init__(self):
super(self.__class__,self).__init__( # fancy way to self-reference
extensionlist=('.nrfd','.ndat'),
strictExtension=False,
formatName = 'q (A-1) step neutron QRE data',
longFormatName = 'q (A-1) stepped neutron text data file in Q,R,E order; E optional'
)
# Validate the contents -- make sure we only have valid lines
[docs]
def ContentsValidator(self, filename):
'Look through the file for expected types of lines in a valid q-step file'
Ndata = 0
fp = open(filename,'r')
for i,S in enumerate(fp):
if '#' in S[0]:
continue
vals = S.split()
if len(vals) >= 2:
try:
data = [float(val) for val in vals]
Ndata += 1
except ValueError:
pass
fp.close()
if not Ndata:
self.errors = 'No 2 or more column numeric data found'
return False
return True # no errors encountered
def Reader(self,filename,filepointer, ParentFrame=None, **unused):
print ('Read a q-step text file')
x = []
y = []
w = []
sq = []
wave = 1.5428 #Cuka default
Temperature = 300
fp = open(filename,'r')
for i,S in enumerate(fp):
if len(S) == 1: #skip blank line
continue
if '=' in S:
self.comments.append(S[:-1])
if 'wave' in S.split('=')[0].lower():
try:
wave = float(S.split('=')[1])
except:
pass
continue
if '#' in S[0]:
continue
vals = S.split()
if len(vals) >= 2:
try:
data = [float(val) for val in vals]
x.append(float(data[0]))
f = float(data[1])
if f <= 0.0:
del x[-1]
continue
elif len(vals) > 2:
y.append(float(data[1]))
w.append(1.0/float(data[2])**2)
if len(vals) == 4:
sq.append(float(data[3]))
else:
sq.append(0.)
else:
y.append(float(data[1]))
w.append(1.0/(0.02*float(data[1]))**2)
sq.append(0.)
except ValueError:
msg = 'Error in line '+str(i+1)
print (msg)
continue
fp.close()
N = len(x)
for S in self.comments:
if 'Temp' in S.split('=')[0]:
try:
Temperature = float(S.split('=')[1])
except:
pass
self.instdict['wave'] = wave
self.instdict['type'] = 'RNC'
x = np.array(x)
self.reflectometrydata = [
x, # x-axis values q
np.array(y), # small angle pattern intensities
np.array(w), # 1/sig(intensity)^2 values (weights)
np.zeros(N), # calc. intensities (zero)
np.zeros(N), # obs-calc profiles
np.array(sq), # Q FWHM
]
self.reflectometryentry[0] = filename
self.reflectometryentry[2] = 1 # xye file only has one bank
self.idstring = ospath.basename(filename)
# scan comments for temperature
self.Sample['Temperature'] = Temperature
return True
[docs]
class txt_XRayThetaReaderClass(G2obj.ImportReflectometryData):
'Routines to import X-ray theta REFD data from a .xtrfd or .xtdat file'
def __init__(self):
super(self.__class__,self).__init__( # fancy way to self-reference
extensionlist=('.xtrfd','.xtdat'),
strictExtension=False,
formatName = 'theta step X-ray QRE data',
longFormatName = 'theta stepped X-ray text data file in Q,R,E order; E optional'
)
# Validate the contents -- make sure we only have valid lines
[docs]
def ContentsValidator(self, filename):
'Look through the file for expected types of lines in a valid q-step file'
Ndata = 0
self.wavelength = 0.
fp = open(filename,'r')
for i,S in enumerate(fp):
if '#' in S[0]:
if 'wavelength' in S[:-1].lower():
self.wavelength = float(S[:-1].split('=')[1])
elif 'energy' in S[:-1].lower():
self.wavelength = 12.39842*1000./float(S[:-1].split('=')[1])
continue
vals = S.split()
if len(vals) >= 2:
try:
data = [float(val) for val in vals]
Ndata += 1
except ValueError:
pass
fp.close()
if not Ndata:
self.errors = 'No 2 or more column numeric data found'
return False
elif not self.wavelength:
self.errors = 'Missing wavelength or energy in header'
return False
return True # no errors encountered
def Reader(self,filename, ParentFrame=None, **unused):
print ('Read a q-step text file')
x = []
y = []
w = []
sq = []
wave = self.wavelength
Temperature = 300
fp = open(filename,'r')
for i,S in enumerate(fp):
if len(S) == 1: #skip blank line
continue
if '=' in S:
self.comments.append(S[:-1])
if 'wave' in S.split('=')[0].lower():
try:
wave = float(S.split('=')[1])
except:
pass
continue
if '#' in S[0]:
continue
vals = S.split()
if len(vals) >= 2:
try:
data = [float(val) for val in vals]
x.append(fourpi*npsind(float(data[0]))/wave)
f = float(data[1])
if f <= 0.0:
del x[-1]
continue
elif len(vals) > 2:
y.append(float(data[1]))
w.append(1.0/float(data[2])**2)
if len(vals) == 4:
sq.append(float(data[3]))
else:
sq.append(0.)
else:
y.append(float(data[1]))
w.append(1.0/(0.02*float(data[1]))**2)
sq.append(0.)
except ValueError:
msg = 'Error in line '+str(i+1)
print (msg)
continue
fp.close()
N = len(x)
for S in self.comments:
if 'Temp' in S.split('=')[0]:
try:
Temperature = float(S.split('=')[1])
except:
pass
self.instdict['wave'] = wave
self.instdict['type'] = 'RXC'
x = np.array(x)
self.reflectometrydata = [
x, # x-axis values q
np.array(y), # small angle pattern intensities
np.array(w), # 1/sig(intensity)^2 values (weights)
np.zeros(N), # calc. intensities (zero)
np.zeros(N), # obs-calc profiles
np.array(sq), # fix bkg
]
self.reflectometryentry[0] = filename
self.reflectometryentry[2] = 1 # xye file only has one bank
self.idstring = ospath.basename(filename)
# scan comments for temperature
self.Sample['Temperature'] = Temperature
return True