Source code for G2rfd_xye

# -*- coding: utf-8 -*-
########### SVN repository information ###################
# $Date: 2020-03-03 21:01:43 +0000 (Tue, 03 Mar 2020) $
# $Author: toby $
# $Revision: 4339 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/imports/G2rfd_xye.py $
# $Id: G2rfd_xye.py 4339 2020-03-03 21:01:43Z toby $
########### SVN repository information ###################
'''
*Module G2rfd_xye: read reflectometry data*
------------------------------------------------

Routines to read in reflectometry data from an .xye type file, with
two-theta or Q steps. 

'''

from __future__ import division, print_function
import os.path as ospath
import numpy as np
import GSASIIobj as G2obj
import GSASIIpath
GSASIIpath.SetVersionNumber("$Revision: 4339 $")
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