Source code for GSASIIfpaGUI

# -*- coding: utf-8 -*-
########### SVN repository information ###################
# $Date: 2021-06-15 18:27:03 +0000 (Tue, 15 Jun 2021) $
# $Author: toby $
# $Revision: 4959 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASIIfpaGUI.py $
# $Id: GSASIIfpaGUI.py 4959 2021-06-15 18:27:03Z toby $
########### SVN repository information ###################
'''
*GSASIIfpaGUI: Fundamental Parameters Routines*
===============================================

This module contains routines for getting Fundamental Parameters 
Approach (FPA) input, setting up for running the NIST XRD Fundamental 
Parameters Code, plotting the convolutors and computing a set of peaks
generated by that code. 

'''
from __future__ import division, print_function
import os.path
import numpy as np
import copy

import wx
import wx.lib.scrolledpanel as wxscroll

import NIST_profile as FP

import GSASIIpath
import GSASIIctrlGUI as G2G
import GSASIIdataGUI as G2gd
import GSASIIplot as G2plt
import GSASIImath as G2mth
import GSASIIpwd as G2pwd
WACV = wx.ALIGN_CENTER_VERTICAL

simParms = {}
'''Parameters to set range for pattern simulation
'''

parmDict = {}
'''Parameter dict used for reading Topas-style values. These are 
converted to SI units and placed into :data:`NISTparms`
'''

NISTparms = {}
'''Parameters in a nested dict, with an entry for each concolutor. Entries in 
those dicts have values in SI units (of course). NISTparms can be 
can be input directly or can be from created from :data:`parmDict`
by :func:`XferFPAsettings`
'''

BraggBrentanoParms = [
    ('divergence', 0.5, 'Bragg-Brentano divergence angle (degrees)'),
    ('soller_angle', 2.0, 'Soller slit axial divergence (degrees)'),
    ('Rs', 220, 'Diffractometer radius (mm)'),
    ('filament_length', 12., 'X-ray tube line focus length (mm)'),
    ('sample_length', 12., 'Illuminated sample length in axial direction (mm)'),
    ('receiving_slit_length', 12., 'Length of receiving slit in axial direction (mm)'),
    ('LAC_cm', 0.,'Linear absorption coef. adjusted for packing density (cm-1)'),
    ('sample_thickness', 1., 'Depth of sample (mm)'),
    ('convolution_steps', 8, 'Number of Fourier-space bins per two-theta step'),
    ('source_width', 0.04,'Tube filament width, in projection at takeoff angle (mm)'),
    ('tube-tails_L-tail', -1.,'Left-side tube tails width, in projection (mm)'),    
    ('tube-tails_R-tail', 1.,'Right-side tube tails width, in projection (mm)'),
    ('tube-tails_rel-I', 0.001,'Tube tails fractional intensity (no units)'),
    ]
'''FPA dict entries used in :func:`FillParmSizer`. Tuple contains
a dict key, a default value and a description. These are the parameters
needed for all Bragg Brentano instruments
'''

BBPointDetector = [
    ('receiving_slit_width', 0.2, 'Width of receiving slit (mm)'),]
'''Additional FPA dict entries used in :func:`FillParmSizer` 
needed for Bragg Brentano instruments with point detectors.
'''

BBPSDDetector = [
    ('lpsd_th2_angular_range', 3.0, 'Angular range observed by PSD (degrees 2Theta)'),
    ('lpsd_equitorial_divergence', 0.1, 'Equatorial divergence of the primary beam (degrees)'),]
'''Additional FPA dict entries used in :func:`FillParmSizer` 
needed for Bragg Brentano instruments with linear (1-D) PSD detectors.
'''

IBmonoParms = [
    ('src_mono_mm',119,'Distance from xray line source to monochromator crystal (mm)'),
    ('focus_mono_mm',217,'Distance from monochromator crystal to focus slit (mm)'),
    ('passband_mistune',-0.145,'Offset from the tuning of the IBM to the center of the reference line of the spectrum, in units of its bandwidth'),
    ('mono_src_proj_mn',51,'Projection width of line-focus xray source on the monochromator along beam direction (microns), sets bandwidth'),
    ('passband_shoulder',.087,'Width of transition region from flat top to tails, in units of the bandwidth'),
    ('two_theta_mono',27.27,'The full diffraction angle of the IBM crystal, e.g. double 2theta-Bragg for the mono (deg)'),
    ('mono_slit_attenuation',0.03,'Attenuation of Cu K alpha2 lines due to focal slit'),
    ]
'''Additional FPA dict entries used in :func:`FillParmSizer`, needed for Incident Beam Monochromator
'''
   
Citation = '''MH Mendenhall, K Mullen && JP Cline (2015), J. Res. of NIST, 120, p223. DOI: 10.6028/jres.120.014

For Incident Beam Mono model, also cite: MH Mendenhall, D. Black && JP Cline, J. Appl. Cryst. (2019), 52, p1087. DOI: 10.1107/S1600576719010951
'''

IBmono = False
'''set to True if an incident beam monochromator is in use
'''
DetMode = 'BBpoint'
'''The type of detector, either 'BBpoint' for Bragg-Brentano point detector or 
      or 'BBPSD' (linear) position sensitive detector
'''

[docs]def SetCu2Wave(): '''Set the parameters to the two-line Cu K alpha 1+2 spectrum ''' parmDict['wave'] = {i:v for i,v in enumerate((1.5405925, 1.5443873))} parmDict['int'] = {i:v for i,v in enumerate((0.653817, 0.346183))} parmDict['lwidth'] = {i:v for i,v in enumerate((0.501844,0.626579))}
[docs]def SetCu6wave(): '''Set the emission parameters to the NIST six-line Cu K alpha spectrum ''' # values from Marcus Mendenhall from atan_windowed_FP_profile.py parmDict['wave'] = {i:v for i,v in enumerate((1.5405925, 1.5443873, 1.5446782, 1.5410769, 1.53471, 1.53382, ))} parmDict['int'] = {i:v for i,v in enumerate((0.58384351, 0.2284605 , 0.11258773, 0.07077796, 0.0043303, 0.00208613, ))} parmDict['lwidth'] = {i:v for i,v in enumerate((0.436, 0.487, 0.63, 0.558, 2.93, 2.93,))}
[docs]def SetMonoWave(): '''Eliminates the short-wavelength line from the six-line Cu K alpha spectrum when incident beam mono; resets it to 6 if no mono ''' if IBmono and len(parmDict['wave']) == 6: for key in 'wave','int','lwidth': if 5 in parmDict[key]: del parmDict[key][5] if 4 in parmDict[key]: del parmDict[key][4] if (not IBmono) and len(parmDict['wave']) == 4: SetCu6wave()
[docs]def writeNIST(filename): '''Write the NIST FPA terms into a JSON-like file that can be reloaded in _onReadFPA ''' if not filename: return fp = open(filename,'w') fp.write('# parameters to be used in the NIST XRD Fundamental Parameters program\n') fp.write('{\n') for key in sorted(NISTparms): fp.write(" '"+key+"' : "+str(NISTparms[key])+",") if not key: fp.write(' # global parameters') fp.write('\n') fp.write('}\n') fp.close()
#SetCu2Wave() # use these as default SetCu6wave() # use these as default SetMonoWave()
[docs]def FillParmSizer(): '''Create a list of input items for the parameter section of the input window, sets default values when not set and displays them in the scrolledpanel prmPnl. ''' prmSizer = prmPnl.GetSizer() prmSizer.Clear(True) if IBmono: itemList = [i for i in BraggBrentanoParms if not i[0].startswith('tube-tails')] else: itemList = copy.deepcopy(BraggBrentanoParms) if DetMode == 'BBpoint': itemList += BBPointDetector elif DetMode == 'BBPSD': itemList += BBPSDDetector else: raise Exception('Unknown DetMode in FillParmSizer: '+DetMode) if IBmono: itemList += IBmonoParms text = wx.StaticText(prmPnl,wx.ID_ANY,'label',style=wx.ALIGN_CENTER, size=(170,-1)) # make just a bit bigger than largest item in column text.SetBackgroundColour(wx.WHITE) prmSizer.Add(text,0,wx.EXPAND) text = wx.StaticText(prmPnl,wx.ID_ANY,'value',style=wx.ALIGN_CENTER) text.SetBackgroundColour(wx.WHITE) prmSizer.Add(text,0,wx.EXPAND) text = wx.StaticText(prmPnl,wx.ID_ANY,'explanation',style=wx.ALIGN_CENTER) text.SetBackgroundColour(wx.WHITE) prmSizer.Add(text,0,wx.EXPAND) for lbl,defVal,text in itemList: prmSizer.Add(wx.StaticText(prmPnl,wx.ID_ANY,lbl),1,wx.ALIGN_RIGHT|WACV,1) if lbl not in parmDict: parmDict[lbl] = defVal ctrl = G2G.ValidatedTxtCtrl(prmPnl,parmDict,lbl,size=(70,-1)) prmSizer.Add(ctrl,1,wx.ALL|WACV,1) txt = wx.StaticText(prmPnl,wx.ID_ANY,text,size=(400,-1)) txt.Wrap(380) prmSizer.Add(txt) px1,py = prmSizer.GetSize() prmSizer.Layout() FPdlg = prmPnl.GetParent() FPdlg.SendSizeEvent()
[docs]def MakeTopasFPASizer(G2frame,FPdlg,SetButtonStatus): '''Create a GUI with parameters for the NIST XRD Fundamental Parameters Code. Parameter input is modeled after Topas input parameters. :param wx.Frame G2frame: main GSAS-II window :param wx.Window FPdlg: Frame or Dialog where GUI will appear :param SetButtonStatus: a callback function to call to see what buttons in this windows can be enabled. Called with done=True to trigger closing the parent window as well. :returns: a sizer with the GUI controls ''' def _onOK(event): XferFPAsettings(parmDict) SetButtonStatus(done=True) # done=True triggers the simulation FPdlg.Destroy() def _onClose(event): SetButtonStatus() FPdlg.Destroy() def _onAddWave(event): newkey = max(parmDict['wave'].keys())+1 for key,defVal in zip( ('wave','int','lwidth'), (0.0, 1.0, 0.1), ): parmDict[key][newkey] = defVal wx.CallAfter(MakeTopasFPASizer,G2frame,FPdlg,SetButtonStatus) def _onRemWave(event): lastkey = max(parmDict['wave'].keys()) for key in ('wave','int','lwidth'): if lastkey in parmDict[key]: del parmDict[key][lastkey] wx.CallAfter(MakeTopasFPASizer,G2frame,FPdlg,SetButtonStatus) def _onSetCu6wave(event): SetCu6wave() SetMonoWave() wx.CallAfter(MakeTopasFPASizer,G2frame,FPdlg,SetButtonStatus) def _onSetCu2Wave(event): SetCu2Wave() wx.CallAfter(MakeTopasFPASizer,G2frame,FPdlg,SetButtonStatus) def _onSetDetBtn(event): global DetMode if detBtn1.GetValue(): DetMode = 'BBpoint' wx.CallAfter(FillParmSizer) else: DetMode = 'BBPSD' wx.CallAfter(FillParmSizer) def _onSetMonoBtn(event): global IBmono IBmono = not monoBtn1.GetValue() SetMonoWave() #wx.CallAfter(FillParmSizer) wx.CallAfter(MakeTopasFPASizer,G2frame,FPdlg,SetButtonStatus) def PlotTopasFPA(event): XferFPAsettings(parmDict) ttArr = np.arange(max(0.5, simParms['plotpos']-simParms['calcwid']), simParms['plotpos']+simParms['calcwid'], simParms['step']) intArr = np.zeros_like(ttArr) NISTpk = setupFPAcalc() try: center_bin_idx,peakObj = doFPAcalc( NISTpk,ttArr,simParms['plotpos'],simParms['calcwid'], simParms['step']) except Exception as err: msg = "Error computing convolution, revise input" print(msg) print(err) return G2plt.PlotFPAconvolutors(G2frame,NISTpk) pkPts = len(peakObj.peak) pkMax = peakObj.peak.max() startInd = center_bin_idx-(pkPts//2) #this should be the aligned start of the new data # scale peak so max I=10,000 and add into intensity array if startInd < 0: intArr[:startInd+pkPts] += 10000 * peakObj.peak[-startInd:]/pkMax elif startInd > len(intArr): return elif startInd+pkPts >= len(intArr): offset = pkPts - len( intArr[startInd:] ) intArr[startInd:startInd+pkPts-offset] += 10000 * peakObj.peak[:-offset]/pkMax else: intArr[startInd:startInd+pkPts] += 10000 * peakObj.peak/pkMax G2plt.PlotXY(G2frame, [(ttArr, intArr)], labelX=r'$2\theta, deg$', labelY=r'Intensity (arbitrary)', Title='FPA peak', newPlot=True, lines=True) def _onSaveFPA(event): XferFPAsettings(parmDict) filename = G2G.askSaveFile(G2frame,'','.NISTfpa', 'dict of NIST FPA values',FPdlg) writeNIST(filename) if FPdlg.GetSizer(): FPdlg.GetSizer().Clear(True) MainSizer = wx.BoxSizer(wx.VERTICAL) MainSizer.Add((-1,5)) waveSizer = wx.FlexGridSizer(cols=len(parmDict['wave'])+1,hgap=3,vgap=5) for lbl,prm,defVal in zip( (u'Wavelength (\u212b)','Rel. Intensity',u'Lorentz Width\n(\u212b/1000)'), ('wave','int','lwidth'), (0.0, 1.0, 0.1), ): text = wx.StaticText(FPdlg,wx.ID_ANY,lbl,style=wx.ALIGN_CENTER) text.SetBackgroundColour(wx.WHITE) waveSizer.Add(text,0,wx.EXPAND) if prm not in parmDict: parmDict[prm] = {} for i in parmDict['wave'].keys(): if i not in parmDict[prm]: parmDict[prm][i] = defVal if prm == 'wave': ctrl = G2G.ValidatedTxtCtrl(FPdlg,parmDict[prm],i,size=(90,-1),nDig=(10,6)) else: ctrl = G2G.ValidatedTxtCtrl(FPdlg,parmDict[prm],i,size=(90,-1),nDig=(10,3)) waveSizer.Add(ctrl,1,WACV,1) MainSizer.Add(waveSizer) MainSizer.Add((-1,5)) btnsizer = wx.BoxSizer(wx.HORIZONTAL) btn = wx.Button(FPdlg, wx.ID_ANY,'Add wave') btnsizer.Add(btn) btn.Bind(wx.EVT_BUTTON,_onAddWave) btn = wx.Button(FPdlg, wx.ID_ANY,'Remove wave') btnsizer.Add(btn) btn.Bind(wx.EVT_BUTTON,_onRemWave) btn = wx.Button(FPdlg, wx.ID_ANY,'CuKa1+2') btnsizer.Add(btn) btn.Bind(wx.EVT_BUTTON,_onSetCu2Wave) btn = wx.Button(FPdlg, wx.ID_ANY,'NIST CuKa') btnsizer.Add(btn) btn.Bind(wx.EVT_BUTTON,_onSetCu6wave) MainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER, 0) MainSizer.Add((-1,5)) btnsizer = wx.GridBagSizer( 2, 5) btnsizer.Add( wx.StaticText(FPdlg, wx.ID_ANY, 'Detector type'), (0,0), (2,1), wx.ALIGN_CENTER | wx.ALL, 5) detBtn1 = wx.RadioButton(FPdlg,wx.ID_ANY,'Point',style=wx.RB_GROUP) detBtn1.SetValue(DetMode == 'BBpoint') btnsizer.Add(detBtn1, (0,1)) detBtn1.Bind(wx.EVT_RADIOBUTTON,_onSetDetBtn) detBtn2 = wx.RadioButton(FPdlg,wx.ID_ANY,'PSD') detBtn2.SetValue(not DetMode == 'BBpoint') btnsizer.Add(detBtn2, (1,1)) detBtn2.Bind(wx.EVT_RADIOBUTTON,_onSetDetBtn) btnsizer.Add( (40,-1), (0,2), (1,1), wx.ALIGN_CENTER | wx.ALL, 5) btnsizer.Add( wx.StaticText(FPdlg, wx.ID_ANY, 'Incident Beam Mono'), (0,3), (2,1), wx.ALIGN_CENTER | wx.ALL, 5) monoBtn1 = wx.RadioButton(FPdlg,wx.ID_ANY,'No',style=wx.RB_GROUP) monoBtn1.SetValue(not IBmono) btnsizer.Add(monoBtn1, (0,4)) monoBtn1.Bind(wx.EVT_RADIOBUTTON,_onSetMonoBtn) monoBtn2 = wx.RadioButton(FPdlg,wx.ID_ANY,'Yes') monoBtn2.SetValue(IBmono) btnsizer.Add(monoBtn2, (1,4)) monoBtn2.Bind(wx.EVT_RADIOBUTTON,_onSetMonoBtn) MainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER, 0) global prmPnl prmPnl = wxscroll.ScrolledPanel(FPdlg, wx.ID_ANY, #size=(200,200), style = wx.TAB_TRAVERSAL|wx.SUNKEN_BORDER) prmSizer = wx.FlexGridSizer(cols=3,hgap=3,vgap=5) prmPnl.SetSizer(prmSizer) FillParmSizer() MainSizer.Add(prmPnl,1,wx.EXPAND,1) prmPnl.SetAutoLayout(1) prmPnl.SetupScrolling() MainSizer.Add((-1,4)) btnsizer = wx.BoxSizer(wx.HORIZONTAL) btn = wx.Button(FPdlg, wx.ID_ANY, 'Plot peak') btnsizer.Add(btn) btn.Bind(wx.EVT_BUTTON,PlotTopasFPA) btnsizer.Add(wx.StaticText(FPdlg,wx.ID_ANY,' at ')) if 'plotpos' not in simParms: simParms['plotpos'] = simParms['minTT'] ctrl = G2G.ValidatedTxtCtrl(FPdlg,simParms,'plotpos',size=(70,-1)) btnsizer.Add(ctrl) btnsizer.Add(wx.StaticText(FPdlg,wx.ID_ANY,' deg. ')) saveBtn = wx.Button(FPdlg, wx.ID_ANY,'Save FPA dict') btnsizer.Add(saveBtn) saveBtn.Bind(wx.EVT_BUTTON,_onSaveFPA) MainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER, 0) MainSizer.Add((-1,4)) btnsizer = wx.BoxSizer(wx.HORIZONTAL) OKbtn = wx.Button(FPdlg, wx.ID_OK) OKbtn.SetDefault() btnsizer.Add(OKbtn) Cbtn = wx.Button(FPdlg, wx.ID_CLOSE,"Cancel") btnsizer.Add(Cbtn) MainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER, 0) MainSizer.Add((-1,4)) # bindings for close of window OKbtn.Bind(wx.EVT_BUTTON,_onOK) Cbtn.Bind(wx.EVT_BUTTON,_onClose) FPdlg.SetSizer(MainSizer) MainSizer.Layout() MainSizer.Fit(FPdlg) # control window size px,py = prmSizer.GetSize() dx,dy = FPdlg.GetSize() FPdlg.SetMinSize((-1,-1)) FPdlg.SetMaxSize((-1,-1)) FPdlg.SetMinSize((dx,dy+200)) # leave a min of 200 points for scroll panel FPdlg.SetMaxSize((max(dx,700),850)) FPdlg.SetSize((max(dx,px+20),min(750,dy+py+30))) # 20 for scroll bar, 30 for a bit of room at bottom
[docs]def XferFPAsettings(InpParms): '''convert Topas-type parameters to SI units for NIST and place in a dict sorted according to use in each convoluter :param dict InpParms: a dict with Topas-like parameters, as set in :func:`MakeTopasFPASizer` :returns: a nested dict with global parameters and those for each convolution ''' # cleanup old stuff for key in "tube_tails","absorption","si_psd","displacement","receiver_slit": if key in NISTparms: del NISTparms[key] keys = list(InpParms['wave'].keys()) source_wavelengths_m = 1.e-10 * np.array([InpParms['wave'][i] for i in keys]) la = [InpParms['int'][i] for i in keys] if IBmono: # kludge: apply mono_slit_attenuation since it is not part of NIST FPA code norm = [InpParms['mono_slit_attenuation'] if (1.5443 < InpParms['wave'][i] < 1.5447) else 1. for i in keys] source_intensities = norm * np.array(la)/max(la) else: source_intensities = np.array(la)/max(la) source_lor_widths_m = 1.e-10 * 1.e-3 * np.array([InpParms['lwidth'][i] for i in keys]) source_gauss_widths_m = 1.e-10 * 1.e-3 * np.array([0.001 for i in keys]) NISTparms["emission"] = {'emiss_wavelengths' : source_wavelengths_m, 'emiss_intensities' : source_intensities, 'emiss_gauss_widths' : source_gauss_widths_m, 'emiss_lor_widths' : source_lor_widths_m, 'crystallite_size_gauss' : 1.e-9 * InpParms.get('Size_G',1e6), 'crystallite_size_lor' : 1.e-9 * InpParms.get('Size_L',1e6)} if IBmono: NISTparms["emission"]['a_mono'] = InpParms['src_mono_mm'] * 10**-3 NISTparms["emission"]['b_mono'] = InpParms['focus_mono_mm'] * 10**-3 NISTparms["emission"]['ibm_source_width'] = InpParms['mono_src_proj_mn'] * 10**-6 for i in ('passband_mistune','passband_shoulder','two_theta_mono'): NISTparms["emission"][i] = InpParms[i] elif InpParms.get('source_width', 0) > 0 and InpParms.get( 'tube-tails_rel-I',0) > 0: NISTparms["tube_tails"] = { 'main_width' : 1e-3 * InpParms.get('source_width', 0.), 'tail_left' : -1e-3 * InpParms.get('tube-tails_L-tail',0.), 'tail_right' : 1e-3 * InpParms.get('tube-tails_R-tail',0.), 'tail_intens' : InpParms.get('tube-tails_rel-I',0.),} if InpParms['filament_length'] == InpParms['receiving_slit_length']: # workaround: InpParms['receiving_slit_length'] *= 1.00001 # avoid bug when slit lengths are identical NISTparms["axial"] = { 'axDiv':"full", 'slit_length_source' : 1e-3*InpParms['filament_length'], 'slit_length_target' : 1e-3*InpParms['receiving_slit_length'], 'length_sample' : 1e-3 * InpParms['sample_length'], 'n_integral_points' : 10, 'angI_deg' : InpParms['soller_angle'], 'angD_deg': InpParms['soller_angle'] } if InpParms.get('LAC_cm',0) > 0: NISTparms["absorption"] = { 'absorption_coefficient': InpParms['LAC_cm']*100, #like LaB6, in m^(-1) 'sample_thickness': 1e-3 * InpParms['sample_thickness'], } if InpParms.get('lpsd_equitorial_divergence',0) > 0 and InpParms.get( 'lpsd_th2_angular_range',0) > 0 and DetMode == 'BBPSD': PSDdetector_length_mm=np.arcsin(np.pi*InpParms['lpsd_th2_angular_range']/180. )*InpParms['Rs'] # mm NISTparms["si_psd"] = { 'equatorial_divergence_deg': InpParms['lpsd_equitorial_divergence'], 'si_psd_window_bounds': (0.,PSDdetector_length_mm/1000.) } if InpParms.get('Specimen_Displacement'): NISTparms["displacement"] = {'specimen_displacement': 1e-3 * InpParms['Specimen_Displacement']} if InpParms.get('receiving_slit_width'): NISTparms["receiver_slit"] = {'slit_width':1e-3*InpParms['receiving_slit_width']} # set Global parameters max_wavelength = source_wavelengths_m[np.argmax(source_intensities)] NISTparms[""] = { 'equatorial_divergence_deg' : InpParms['divergence'], 'dominant_wavelength' : max_wavelength, 'diffractometer_radius' : 1e-3* InpParms['Rs'], 'oversampling' : InpParms['convolution_steps'], }
[docs]def setupFPAcalc(): '''Create a peak profile object using the NIST XRD Fundamental Parameters Code. :returns: a profile object that can provide information on each convolution or compute the composite peak shape. ''' if IBmono: p=FP.FP_windowed(anglemode="twotheta", output_gaussian_smoother_bins_sigma=1.0, oversampling=NISTparms.get('oversampling',10)) else: p=FP.FP_profile(anglemode="twotheta", output_gaussian_smoother_bins_sigma=1.0, oversampling=NISTparms.get('oversampling',10)) p.debug_cache=False #set parameters for each convolver for key in NISTparms: if key: p.set_parameters(convolver=key,**NISTparms[key]) else: p.set_parameters(**NISTparms[key]) return p
[docs]def doFPAcalc(NISTpk,ttArr,twotheta,calcwid,step): '''Compute a single peak using a NIST profile object :param object NISTpk: a peak profile computational object from the NIST XRD Fundamental Parameters Code, typically established from a call to :func:`SetupFPAcalc` :param np.Array ttArr: an evenly-spaced grid of two-theta points (degrees) :param float twotheta: nominal center of peak (degrees) :param float calcwid: width to perform convolution (degrees) :param float step: step size ''' # find closest point to twotheta (may be outside limits of the array) center_bin_idx=min(ttArr.searchsorted(twotheta),len(ttArr)-1) NISTpk.set_optimized_window(twotheta_exact_bin_spacing_deg=step, twotheta_window_center_deg=ttArr[center_bin_idx], twotheta_approx_window_fullwidth_deg=calcwid, ) NISTpk.set_parameters(twotheta0_deg=twotheta) return center_bin_idx,NISTpk.compute_line_profile()
[docs]def MakeSimSizer(G2frame, dlg): '''Create a GUI to get simulation with parameters for Fundamental Parameters fitting. :param wx.Window dlg: Frame or Dialog where GUI will appear :returns: a sizer with the GUI controls ''' def _onOK(event): msg = '' if simParms['minTT']-simParms['calcwid']/1.5 < 0.1: msg += 'First peak minus half the calc width is too low' if simParms['maxTT']+simParms['calcwid']/1.5 > 175: if msg: msg += '\n' msg += 'Last peak plus half the calc width is too high' if simParms['npeaks'] < 8: if msg: msg += '\n' msg += 'At least 8 peaks are needed' if msg: G2G.G2MessageBox(dlg,msg,'Bad input, try again') return # compute "obs" pattern ttArr = np.arange(max(0.5, simParms['minTT']-simParms['calcwid']/1.5), simParms['maxTT']+simParms['calcwid']/1.5, simParms['step']) intArr = np.zeros_like(ttArr) peaklist = np.linspace(simParms['minTT'],simParms['maxTT'], simParms['npeaks'],endpoint=True) peakSpacing = (peaklist[-1]-peaklist[0])/(len(peaklist)-1) NISTpk = setupFPAcalc() minPtsHM = len(intArr) # initialize points above half-max maxPtsHM = 0 for num,twoth_peak in enumerate(peaklist): try: center_bin_idx,peakObj = doFPAcalc( NISTpk,ttArr,twoth_peak,simParms['calcwid'], simParms['step']) except Exception as err: if msg: msg += '\n' msg = "Error computing convolution, revise input. Error =\n"+str(err) continue if num == 0: G2plt.PlotFPAconvolutors(G2frame,NISTpk) pkMax = peakObj.peak.max() pkPts = len(peakObj.peak) minPtsHM = min(minPtsHM,sum(peakObj.peak >= 0.5*pkMax)) # points above half-max maxPtsHM = max(maxPtsHM,sum(peakObj.peak >= 0.5*pkMax)) # points above half-max startInd = center_bin_idx-(pkPts//2) #this should be the aligned start of the new data # scale peak so max I=10,000 and add into intensity array if startInd < 0: intArr[:startInd+pkPts] += 10000 * peakObj.peak[-startInd:]/pkMax elif startInd > len(intArr): break elif startInd+pkPts >= len(intArr): offset = pkPts - len( intArr[startInd:] ) intArr[startInd:startInd+pkPts-offset] += 10000 * peakObj.peak[:-offset]/pkMax else: intArr[startInd:startInd+pkPts] += 10000 * peakObj.peak/pkMax # check if peaks are too closely spaced if maxPtsHM*simParms['step'] > peakSpacing/4: if msg: msg += '\n' msg += 'Maximum FWHM ({}) is too large compared to the peak spacing ({}). Decrease number of peaks or increase data range.'.format( maxPtsHM*simParms['step'], peakSpacing) # check if too few points across Hmax if minPtsHM < 10: if msg: msg += '\n' msg += 'There are only {} points above the half-max. 10 are needed. Dropping step size.'.format(minPtsHM) simParms['step'] *= 0.5 if msg: G2G.G2MessageBox(dlg,msg,'Bad input, try again') wx.CallAfter(MakeSimSizer,G2frame, dlg) return # pattern has been computed successfully dlg.Destroy() wx.CallAfter(FitFPApeaks,ttArr, intArr, peaklist, maxPtsHM) # do peakfit outside event callback def FitFPApeaks(ttArr, intArr, peaklist, maxPtsHM): '''Perform a peak fit to the FP simulated pattern ''' pgbar = wx.ProgressDialog('FPA Simulation','Starting FPA simulation',100, parent=G2frame, style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE #|wx.PD_CAN_ABORT ) pgbar.Raise() wx.BeginBusyCursor() # pick out one or two most intense wavelengths ints = list(NISTparms['emission']['emiss_intensities']) Lam1 = NISTparms['emission']['emiss_wavelengths'][np.argmax(ints)]*1e10 if 'two_theta_mono' in NISTparms['emission']: # is there an IBM? Lam2 = None # Yes, ~monochromatic else: # get lambda 2 ints[np.argmax(ints)] = -1 Lam2 = NISTparms['emission']['emiss_wavelengths'][np.argmax(ints)]*1e10 histId = G2frame.AddSimulatedPowder(ttArr,intArr, 'NIST Fundamental Parameters simulation', Lam1,Lam2) controls = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Controls')) controldat = controls.get('data', {'deriv type':'analytic','min dM/M':0.001,}) #fil Parms,Parms2 = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,histId,'Instrument Parameters')) peakData = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,histId,'Peak List')) # set background to 0 with one term = 0; disable refinement bkg1,bkg2 = bkg = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,histId,'Background')) bkg1[1]=False bkg1[2]=0 bkg1[3]=0.0 limits = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,histId,'Limits')) # approximate asym correction try: Parms['SH/L'][1] = 0.25 * ( NISTparms['axial']['length_sample']+ NISTparms['axial']['slit_length_source'] ) / NISTparms['']['diffractometer_radius'] except: pass pgbar.Update(5,newmsg='Creating peak list') pgbar.Raise() for pos in peaklist: i = ttArr.searchsorted(pos) area = sum(intArr[max(0,i-maxPtsHM):min(len(intArr),i+maxPtsHM)]) peakData['peaks'].append(G2mth.setPeakparms(Parms,Parms2,pos,area)) pgbar.Update(10,newmsg='Refining peak positions') histData = G2frame.GPXtree.GetItemPyData(histId) # refine peak positions only bxye = np.zeros(len(histData[1][1])) peakData['sigDict'] = G2pwd.DoPeakFit('LSQ',peakData['peaks'], bkg,limits[1],Parms,Parms2,histData[1],bxye,[],False,controldat)[0] pgbar.Update(20,newmsg='Refining peak positions && areas') # refine peak areas as well for pk in peakData['peaks']: pk[1] = True peakData['sigDict'] = G2pwd.DoPeakFit('LSQ',peakData['peaks'], bkg,limits[1],Parms,Parms2,histData[1],bxye,[],False,controldat)[0] pgbar.Update(40,newmsg='Refining profile function') # refine profile function for p in ('U', 'V', 'W', 'X', 'Y'): Parms[p][2] = True peakData['sigDict'] = G2pwd.DoPeakFit('LSQ',peakData['peaks'], bkg,limits[1],Parms,Parms2,histData[1],bxye,[],False,controldat)[0] pgbar.Update(70,newmsg='Refining profile function && asymmetry') # add in asymmetry Parms['SH/L'][2] = True peakData['sigDict'] = G2pwd.DoPeakFit('LSQ',peakData['peaks'], bkg,limits[1],Parms,Parms2,histData[1],bxye,[],False,controldat)[0] pgbar.Update(100,newmsg='Done') # reset "initial" profile for p in Parms: if len(Parms[p]) == 3: Parms[p][0] = Parms[p][1] Parms[p][2] = False pgbar.Destroy() wx.EndBusyCursor() # save Iparms pth = G2G.GetExportPath(G2frame) fldlg = wx.FileDialog(G2frame, 'Set name to save GSAS-II instrument parameters file', pth, '', 'instrument parameter files (*.instprm)|*.instprm',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT) try: if fldlg.ShowModal() == wx.ID_OK: filename = fldlg.GetPath() # make sure extension is .instprm filename = os.path.splitext(filename)[0]+'.instprm' File = open(filename,'w') File.write("#GSAS-II instrument parameter file; do not add/delete items!\n") for item in Parms: File.write(item+':'+str(Parms[item][1])+'\n') File.close() print ('Instrument parameters saved to: '+filename) finally: fldlg.Destroy() #GSASIIpath.IPyBreak() def _onClose(event): dlg.Destroy() def SetButtonStatus(done=False): OKbtn.Enable(bool(NISTparms)) #saveBtn.Enable(bool(NISTparms)) if done: _onOK(None) def _onSetFPA(event): # Create a non-modal dialog for Topas-style FP input. FPdlg = wx.Dialog(dlg,wx.ID_ANY,'FPA parameters', style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER) MakeTopasFPASizer(G2frame,FPdlg,SetButtonStatus) FPdlg.CenterOnParent() FPdlg.Raise() FPdlg.Show() def _onSaveFPA(event): filename = G2G.askSaveFile(G2frame,'','.NISTfpa', 'dict of NIST FPA values',dlg) writeNIST(filename) def _onReadFPA(event): filename = G2G.GetImportFile(G2frame, message='Read file with dict of values for NIST Fundamental Parameters', parent=dlg, wildcard='dict of NIST FPA values|*.NISTfpa') if not filename: return if not filename[0]: return try: txt = open(filename[0],'r').read() NISTparms.clear() d = eval(txt) NISTparms.update(d) except Exception as err: G2G.G2MessageBox(dlg, u'Error reading file {}:{}\n'.format(filename,err), 'Bad dict input') #GSASIIpath.IPyBreak() SetButtonStatus() if dlg.GetSizer(): dlg.GetSizer().Clear(True) MainSizer = wx.BoxSizer(wx.VERTICAL) MainSizer.Add(wx.StaticText(dlg,wx.ID_ANY, 'Fit Profile Parameters to Peaks from Fundamental Parameters', style=wx.ALIGN_CENTER),0,wx.EXPAND) MainSizer.Add((-1,5)) prmSizer = wx.FlexGridSizer(cols=2,hgap=3,vgap=5) text = wx.StaticText(dlg,wx.ID_ANY,'value',style=wx.ALIGN_CENTER) text.SetBackgroundColour(wx.WHITE) prmSizer.Add(text,0,wx.EXPAND) text = wx.StaticText(dlg,wx.ID_ANY,'explanation',style=wx.ALIGN_CENTER) text.SetBackgroundColour(wx.WHITE) prmSizer.Add(text,0,wx.EXPAND) for key,defVal,text in ( ('minTT',3.,'Location of first peak in 2theta (deg)'), ('maxTT',123.,'Location of last peak in 2theta (deg)'), ('step',0.01,'Pattern step size (deg 2theta)'), ('npeaks',13,'Number of peaks'), ('calcwid',2.,'Range to compute each peak (deg 2theta)'), ): if key not in simParms: simParms[key] = defVal ctrl = G2G.ValidatedTxtCtrl(dlg,simParms,key,size=(70,-1)) prmSizer.Add(ctrl,1,wx.ALL|WACV,1) txt = wx.StaticText(dlg,wx.ID_ANY,text,size=(300,-1)) txt.Wrap(280) prmSizer.Add(txt) MainSizer.Add(prmSizer) btnsizer = wx.BoxSizer(wx.HORIZONTAL) btn = wx.Button(dlg, wx.ID_ANY,'Input FP vals') btnsizer.Add(btn) btn.Bind(wx.EVT_BUTTON,_onSetFPA) #saveBtn = wx.Button(dlg, wx.ID_ANY,'Save FPA dict') #btnsizer.Add(saveBtn) #saveBtn.Bind(wx.EVT_BUTTON,_onSaveFPA) readBtn = wx.Button(dlg, wx.ID_ANY,'Read FPA dict') btnsizer.Add(readBtn) readBtn.Bind(wx.EVT_BUTTON,_onReadFPA) MainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER, 0) MainSizer.Add((-1,4),1,wx.EXPAND,1) txt = wx.StaticText(dlg,wx.ID_ANY,'If you use this, please cite: '+Citation,size=(350,-1)) txt.Wrap(340) MainSizer.Add(txt,0,wx.ALIGN_CENTER) btnsizer = wx.BoxSizer(wx.HORIZONTAL) OKbtn = wx.Button(dlg, wx.ID_OK) OKbtn.SetDefault() btnsizer.Add(OKbtn) Cbtn = wx.Button(dlg, wx.ID_CLOSE,"Cancel") btnsizer.Add(Cbtn) MainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER, 0) MainSizer.Add((-1,4),1,wx.EXPAND,1) # bindings for close of window OKbtn.Bind(wx.EVT_BUTTON,_onOK) Cbtn.Bind(wx.EVT_BUTTON,_onClose) SetButtonStatus() dlg.SetSizer(MainSizer) MainSizer.Layout() MainSizer.Fit(dlg) dlg.SetMinSize(dlg.GetSize()) dlg.SendSizeEvent() dlg.Raise()
def GetFPAInput(G2frame): dlg = wx.Dialog(G2frame,wx.ID_ANY,'FPA input', style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER) MakeSimSizer(G2frame,dlg) dlg.CenterOnParent() dlg.Show() return if __name__ == "__main__": app = wx.PySimpleApp() GSASIIpath.InvokeDebugOpts() frm = wx.Frame(None) # create a frame frm.Show(True) frm.TutorialImportDir = '/tmp' GetFPAInput(frm) app.MainLoop()