Source code for GSASIIimgGUI

# -*- coding: utf-8 -*-
#GSASII - image data display routines
########### SVN repository information ###################
# $Date: 2021-08-05 12:43:13 +0000 (Thu, 05 Aug 2021) $
# $Author: vondreele $
# $Revision: 5008 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASIIimgGUI.py $
# $Id: GSASIIimgGUI.py 5008 2021-08-05 12:43:13Z vondreele $
########### SVN repository information ###################
'''
*GSASIIimgGUI: Image GUI*
-------------------------

Control image display and processing

'''
from __future__ import division, print_function
import os
import copy
import glob
import time
import re
import math
import sys
import wx
import wx.lib.mixins.listctrl  as  listmix
import wx.grid as wg
import matplotlib as mpl
import numpy as np
import numpy.ma as ma
import GSASIIpath
GSASIIpath.SetVersionNumber("$Revision: 5008 $")
import GSASIIimage as G2img
import GSASIImath as G2mth
import GSASIIElem as G2elem
import GSASIIpwdGUI as G2pdG
import GSASIIplot as G2plt
import GSASIIIO as G2IO
import GSASIIfiles as G2fil
import GSASIIdataGUI as G2gd
import GSASIIctrlGUI as G2G
import GSASIIobj as G2obj
import GSASIIpy3 as G2py3
import ImageCalibrants as calFile

# documentation build kludge. This prevents an error with sphinx 1.8.5 (fixed by 2.3) where all mock objects are of type _MockObject
if (type(wx.ListCtrl).__name__ ==
        type(listmix.ListCtrlAutoWidthMixin).__name__ ==
        type(listmix.TextEditMixin).__name__):
    print('Using Sphinx 1.8.5 _MockObject kludge fix in GSASIIimgGUI')
    class Junk1(object): pass
    listmix.ListCtrlAutoWidthMixin = Junk1
    class Junk2(object): pass
    listmix.TextEditMixin = Junk2

VERY_LIGHT_GREY = wx.Colour(235,235,235)
WACV = wx.ALIGN_CENTER_VERTICAL

# trig functions in degrees
sind = lambda x: math.sin(x*math.pi/180.)
tand = lambda x: math.tan(x*math.pi/180.)
cosd = lambda x: math.cos(x*math.pi/180.)
asind = lambda x: 180.*math.asin(x)/math.pi
tth2q = lambda t,w:4.0*math.pi*sind(t/2.0)/w
tof2q = lambda t,C:2.0*math.pi*C/t
atand = lambda x: 180.*math.atan(x)/math.pi
atan2d = lambda y,x: 180.*math.atan2(y,x)/math.pi

################################################################################
##### Image Data
################################################################################

[docs]def GetImageZ(G2frame,data,newRange=False): '''Gets image & applies dark, background & flat background corrections. :param wx.Frame G2frame: main GSAS-II frame :param: dict data: Image Controls dictionary :returns: array sumImg: corrected image for background/dark/flat back ''' # Note that routine GSASIIscriptable._getCorrImage is based on this # so changes made here should be repeated there. Npix,imagefile,imagetag = G2IO.GetCheckImageFile(G2frame,G2frame.Image) if imagefile is None: return [] formatName = data.get('formatName','') sumImg = np.array(G2IO.GetImageData(G2frame,imagefile,True,ImageTag=imagetag,FormatName=formatName),dtype='int32') if sumImg is None: return [] darkImg = False if 'dark image' in data: darkImg,darkScale = data['dark image'] if darkImg: Did = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, darkImg) if Did: Ddata = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Did,'Image Controls')) dformatName = Ddata.get('formatName','') Npix,darkfile,imagetag = G2IO.GetCheckImageFile(G2frame,Did) darkImage = G2IO.GetImageData(G2frame,darkfile,True,ImageTag=imagetag,FormatName=dformatName) if darkImg is not None: sumImg += np.array(darkImage*darkScale,dtype='int32') else: print('Warning: resetting dark image (not found: {})'.format( darkImg)) data['dark image'][0] = darkImg = '' if 'background image' in data: backImg,backScale = data['background image'] if backImg: #ignores any transmission effect in the background image Bid = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, backImg) if Bid: Npix,backfile,imagetag = G2IO.GetCheckImageFile(G2frame,Bid) Bdata = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Bid,'Image Controls')) bformatName = Bdata.get('formatName','') backImage = G2IO.GetImageData(G2frame,backfile,True,ImageTag=imagetag,FormatName=bformatName) if darkImg and backImage is not None: backImage += np.array(darkImage*darkScale/backScale,dtype='int32') if backImage is not None: sumImg += np.array(backImage*backScale,dtype='int32') if 'Gain map' in data: gainMap = data['Gain map'] if gainMap: GMid = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, gainMap) if GMid: Npix,gainfile,imagetag = G2IO.GetCheckImageFile(G2frame,GMid) Gdata = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,GMid,'Image Controls')) gformat = Gdata['formatName'] GMimage = G2IO.GetImageData(G2frame,gainfile,True,ImageTag=imagetag,FormatName=gformat) sumImg = sumImg*GMimage/1000 sumImg -= int(data.get('Flat Bkg',0)) Imax = np.max(sumImg) if 'range' not in data or newRange: data['range'] = [(0,Imax),[0,Imax]] return np.asarray(sumImg,dtype='int32')
def UpdateImageData(G2frame,data): def OnPixVal(invalid,value,tc): G2plt.PlotExposedImage(G2frame,newPlot=True,event=tc.event) def OnPolaCalib(event): if data['IOtth'][1] < 34.: G2G.G2MessageBox(G2frame,'Maximum 2-theta not greater than 34 deg', 'Polarization Calibration Error') return IOtth = [32.,data['IOtth'][1]-2.] dlg = G2G.SingleFloatDialog(G2frame,'Polarization test arc mask', ''' Do not use if pattern has uneven absorption Set 2-theta max in image controls to be fully inside image Enter 2-theta position for arc mask (32-%.1f) '''%IOtth[1],IOtth[1],IOtth,fmt='%.2f') if dlg.ShowModal() == wx.ID_OK: arcTth = dlg.GetValue() G2fil.G2SetPrintLevel('none') G2img.DoPolaCalib(G2frame.ImageZ,data,arcTth) G2fil.G2SetPrintLevel('all') UpdateImageData(G2frame,data) dlg.Destroy() def OnMakeGainMap(event): import scipy.ndimage.filters as sdif sumImg = GetImageZ(G2frame,data) masks = copy.deepcopy(G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.Image,'Masks'))) Data = copy.deepcopy(data) #force defaults for GainMap calc Data['IOtth'] = [0.1,60.0] Data['outAzimuths'] = 1 Data['LRazimuth'] = [0.,360.] Data['outChannels'] = 5000 Data['binType'] = '2-theta' Data['color'] = 'gray' G2frame.Integrate = G2img.ImageIntegrate(sumImg,Data,masks,blkSize) Iy,azms,Ix = G2frame.Integrate[:3] GainMap = G2img.MakeGainMap(sumImg,Ix,Iy,Data,blkSize)*1000. Npix,imagefile,imagetag = G2IO.GetCheckImageFile(G2frame,G2frame.Image) pth = os.path.split(os.path.abspath(imagefile))[0] outname = 'GainMap' dlg = wx.FileDialog(G2frame, 'Choose gain map filename', pth,outname, 'G2img files (*.G2img)|*.G2img',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT) if dlg.ShowModal() == wx.ID_OK: newimagefile = dlg.GetPath() newimagefile = G2IO.FileDlgFixExt(dlg,newimagefile) Data['formatName'] = 'GSAS-II image' Data['range'] = [(500,2000),[800,1200]] GainMap = np.where(GainMap > 2000,2000,GainMap) GainMap = np.where(GainMap < 500,500,GainMap) masks['Thresholds'] = [(500.,2000.),[800.,1200.]] G2IO.PutG2Image(newimagefile,[],data,Npix,GainMap) GMname = 'IMG '+os.path.split(newimagefile)[1] Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,GMname) if not Id: Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=GMname) G2frame.GPXtree.SetItemPyData(Id,[Npix,newimagefile]) G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),[]) G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Image Controls'),Data) G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Masks'),masks) else: G2frame.GPXtree.SetItemPyData(Id,[Npix,newimagefile]) G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Comments'),[]) G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Image Controls'),Data) G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Masks'),masks) G2frame.GPXtree.Expand(Id) G2frame.GPXtree.SelectItem(Id) #to show the gain map & put it in the list G2frame.dataWindow.ClearData() G2frame.ImageZ = GetImageZ(G2frame,data) mainSizer = G2frame.dataWindow.GetSizer() mainSizer.Add(wx.StaticText(G2frame.dataWindow, label='Do not change anything here unless you are absolutely sure!'),0) mainSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Image size: %d by %d'%(data['size'][0],data['size'][1])),0) pixSize = wx.FlexGridSizer(0,4,5,5) pixLabels = [u' Pixel X-dimension (\xb5m)',u' Pixel Y-dimension (\xb5m)'] for i,[pixLabel,pix] in enumerate(zip(pixLabels,data['pixelSize'])): pixSize.Add(wx.StaticText(G2frame.dataWindow,label=pixLabel),0,WACV) pixVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['pixelSize'],i,nDig=(10,3), typeHint=float,OnLeave=OnPixVal) pixSize.Add(pixVal,0,WACV) mainSizer.Add(pixSize,0) distSizer = wx.BoxSizer(wx.HORIZONTAL) distSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Set detector distance: '),0,WACV) if 'setdist' not in data: data['setdist'] = data['distance'] distSizer.Add(G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'setdist',nDig=(10,4), typeHint=float),0,WACV) distSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Polarization: '),0,WACV) if 'PolaVal' not in data: #patch data['PolaVal'] = [0.99,False] distSizer.Add(G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['PolaVal'],0,nDig=(10,4), xmin=0.,xmax=1.,typeHint=float),0,WACV) polaCalib = wx.Button(G2frame.dataWindow,label='Calibrate?') polaCalib.Bind(wx.EVT_BUTTON,OnPolaCalib) distSizer.Add(polaCalib,0,WACV) mainSizer.Add(distSizer,0) #patch if 'samplechangerpos' not in data or data['samplechangerpos'] is None: data['samplechangerpos'] = 0.0 if 'det2theta' not in data: data['det2theta'] = 0.0 if 'Gain map' not in data: data['Gain map'] = '' #end patch tthSizer = wx.BoxSizer(wx.HORIZONTAL) tthSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Detector 2-theta: '),0,WACV) tthSizer.Add(G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'det2theta',xmin=-180.,xmax=180.,nDig=(10,2)),0,WACV) tthSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Sample changer position %.2f mm '%data['samplechangerpos']),0,WACV) mainSizer.Add(tthSizer,0) if not data['Gain map']: makeGain = wx.Button(G2frame.dataWindow,label='Make gain map from this image? NB: use only an amorphous pattern for this') makeGain.Bind(wx.EVT_BUTTON,OnMakeGainMap) mainSizer.Add(makeGain) G2frame.dataWindow.SetDataSize() ################################################################################ ##### Image Controls ################################################################################ blkSize = 128 #128 seems to be optimal; will break in polymask if >1024
[docs]def UpdateImageControls(G2frame,data,masks,useTA=None,useMask=None,IntegrateOnly=False): '''Shows and handles the controls on the "Image Controls" data tree entry ''' #patch if 'Flat Bkg' not in data: data['Flat Bkg'] = 0.0 if 'Gain map' not in data: data['Gain map'] = '' if 'GonioAngles' not in data: data['GonioAngles'] = [0.,0.,0.] if 'DetDepth' not in data: data['DetDepth'] = 0. if 'SampleAbs' not in data: data['SampleShape'] = 'Cylinder' data['SampleAbs'] = [0.0,False] if 'binType' not in data: if 'PWDR' in data['type']: data['binType'] = '2-theta' elif 'SASD' in data['type']: data['binType'] = 'log(q)' if 'varyList' not in data: data['varyList'] = {'dist':True,'det-X':True,'det-Y':True,'tilt':True,'phi':True,'dep':False,'wave':False} if data['DetDepth'] > 0.5: data['DetDepth'] /= data['distance'] if 'setdist' not in data: data['setdist'] = data['distance'] if 'linescan' not in data: data['linescan'] = [False,0.0] #includes azimuth to draw line scan if 'det2theta' not in data: data['det2theta'] = 0.0 if 'orientation' not in data: data['orientation'] = 'horizontal' #end patch # Menu items def OnCalibrate(event): if not data['calibrant']: G2G.G2MessageBox(G2frame,'No calibrant material specified.\n'+ 'Please correct this and try again.') return G2frame.GetStatusBar().SetStatusText('Select > 4 points on 1st used ring; LB to pick (shift key to force pick), RB on point to delete else RB to finish',1) G2frame.ifGetRing = True def OnRecalibrate(event): '''Use existing calibration values as starting point for a calibration fit ''' G2img.ImageRecalibrate(G2frame,G2frame.ImageZ,data,masks) wx.CallAfter(UpdateImageControls,G2frame,data,masks) def OnRecalibAll(event): '''Use existing calibration values as starting point for a calibration fit for a selected series of images ''' Id = None Names = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',]) dlg = G2G.G2MultiChoiceDialog(G2frame,'Image calibration controls','Select images to recalibrate:',Names) try: if dlg.ShowModal() == wx.ID_OK: Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Sequential image calibration results') if Id: SeqResult = G2frame.GPXtree.GetItemPyData(Id) else: Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text='Sequential image calibration results') SeqResult = {'SeqPseudoVars':{},'SeqParFitEqList':[]} items = dlg.GetSelections() G2frame.EnablePlot = False for item in items: name = Names[item] print ('calibrating'+name) G2frame.Image = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,name) Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.Image,'Image Controls')) G2frame.ImageZ = GetImageZ(G2frame,Data) Data['setRings'] = True Mid = G2gd.GetGPXtreeItemId(G2frame,G2frame.Image,'Masks') Masks = G2frame.GPXtree.GetItemPyData(Mid) result = G2img.ImageRecalibrate(G2frame,G2frame.ImageZ,Data,Masks) if not len(result): print('calibrant missing from local image calibrants files') return vals,varyList,sigList,parmDict,covar = result sigList = list(sigList) if 'dist' not in varyList: vals.append(parmDict['dist']) varyList.append('dist') sigList.append(None) vals.append(Data.get('setdist',Data['distance'])) # add setdist to varylist etc. so that it is displayed in Seq Res table varyList.append('setdist') sigList.append(None) covar = np.lib.pad(covar, (0,1), 'constant') # vals.append(Data.get('samplechangerpos',Data['samplechangerpos'])) # varyList.append('chgrpos') # sigList.append(None) SeqResult[name] = {'variables':vals,'varyList':varyList,'sig':sigList,'Rvals':[], 'covMatrix':covar,'title':name,'parmDict':parmDict} SeqResult['histNames'] = Names G2frame.GPXtree.SetItemPyData(Id,SeqResult) finally: dlg.Destroy() print ('All selected images recalibrated - results in Sequential image calibration results') G2frame.G2plotNB.Delete('Sequential refinement') #clear away probably invalid plot G2plt.PlotExposedImage(G2frame,event=None) if Id: G2frame.GPXtree.SelectItem(Id) def OnDistRecalib(event): '''Assemble rings & calibration input for a series of images with differing distances ''' obsArr = np.array([]).reshape(0,4) parmDict = {} varList = [] HKL = {} Names = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',]) startID = G2frame.GPXtree.GetSelection() dlg = G2G.G2MultiChoiceDialog(G2frame,'Image calibration controls','Select images to recalibrate:',Names) try: if dlg.ShowModal() == wx.ID_OK: wx.BeginBusyCursor() items = dlg.GetSelections() print('Scanning for ring picks...') # G2frame.EnablePlot = False for item in items: name = Names[item] print ('getting rings for',name) G2frame.Image = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,name) Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.Image,'Image Controls')) key = str(int(Data['setdist'])) # create a parameter dict for combined fit if 'wavelength' not in parmDict: parmDict['wavelength'] = Data['wavelength'] if Data['varyList']['wave']: varList += ['wavelength'] if Data['varyList']['dist']: G2G.G2MessageBox(G2frame, 'You cannot vary individual detector positions and the global wavelength.\n\nChange flags for 1st image.', 'Conflicting vars') return parmDict['dep'] = Data['DetDepth'] if Data['varyList']['dep']: varList += ['dep'] # distance flag determines if individual values are refined if not Data['varyList']['dist']: # starts as zero, single variable, always refined parmDict['deltaDist'] = 0. varList += ['deltaDist'] parmDict['phi'] = Data['rotation'] if Data['varyList']['phi']: varList += ['phi'] parmDict['tilt'] = Data['tilt'] if Data['varyList']['tilt']: varList += ['tilt'] G2frame.ImageZ = GetImageZ(G2frame,Data) Data['setRings'] = True Mid = G2gd.GetGPXtreeItemId(G2frame,G2frame.Image,'Masks') Masks = G2frame.GPXtree.GetItemPyData(Mid) result = G2img.ImageRecalibrate(G2frame,G2frame.ImageZ,Data,Masks,getRingsOnly=True) if not len(result): print('calibrant missing from local image calibrants files') return rings,HKL[key] = result # add detector set dist into data array, create a single really large array distarr = np.zeros_like(rings[:,2:3]) if 'setdist' not in Data: print('Distance (setdist) not in image metadata') return distarr += Data['setdist'] obsArr = np.concatenate(( obsArr, np.concatenate((rings[:,0:2],distarr,rings[:,2:3]),axis=1)),axis=0) if 'deltaDist' not in parmDict: # starts as zero, variable refined for each image parmDict['delta'+key] = 0 varList += ['delta'+key] for i,z in enumerate(['X','Y']): v = 'det-'+z if v+key in parmDict: print('Error: two images with setdist ~=',key) return parmDict[v+key] = Data['center'][i] if Data['varyList'][v]: varList += [v+key] #GSASIIpath.IPyBreak() print('\nFitting',obsArr.shape[0],'ring picks and',len(varList),'variables...') result = G2img.FitMultiDist(obsArr,varList,parmDict,covar=True) covar = result[3] covData = {'title':'Multi-distance recalibrate','covMatrix':covar,'varyList':varList,'variables':result[1]} Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Covariance') G2frame.GPXtree.SetItemPyData(Id,covData) for item in items: name = Names[item] print ('updating',name) G2frame.Image = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,name) Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.Image,'Image Controls')) Data['wavelength'] = parmDict['wavelength'] key = str(int(Data['setdist'])) Data['center'] = [parmDict['det-X'+key],parmDict['det-Y'+key]] if 'deltaDist' in parmDict: Data['distance'] = Data['setdist'] - parmDict['deltaDist'] else: Data['distance'] = Data['setdist'] - parmDict['delta'+key] Data['rotation'] = np.mod(parmDict['phi'],360.0) Data['tilt'] = parmDict['tilt'] Data['DetDepth'] = parmDict['dep'] #Data['chisq'] = chisq N = len(Data['ellipses']) Data['ellipses'] = [] #clear away individual ellipse fits for H in HKL[key][:N]: ellipse = G2img.GetEllipse(H[3],Data) Data['ellipses'].append(copy.deepcopy(ellipse+('b',))) G2frame.EnablePlot = True G2frame.GPXtree.SelectItem(G2frame.root) # there is probably a better way to force the reload of the current page wx.CallAfter(G2frame.GPXtree.SelectItem,startID) #GSASIIpath.IPyBreak() # create a sequential table? # Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Sequential image calibration results') # if Id: # SeqResult = G2frame.GPXtree.GetItemPyData(Id) # else: # Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text='Sequential image calibration results') #SeqResult = {'SeqPseudoVars':{},'SeqParFitEqList':[]} # vals,varyList,sigList,parmDict,covar = result # sigList = list(sigList) # if 'dist' not in varyList: # vals.append(parmDict['dist']) # varyList.append('dist') # sigList.append(None) # vals.append(Data.get('setdist',Data['distance'])) # # add setdist to varylist etc. so that it is displayed in Seq Res table # varyList.append('setdist') # sigList.append(None) # covar = np.lib.pad(covar, (0,1), 'constant') # vals.append(Data.get('samplechangerpos',Data['samplechangerpos'])) # varyList.append('chgrpos') # sigList.append(None) # SeqResult[name] = {'variables':vals,'varyList':varyList,'sig':sigList,'Rvals':[], # 'covMatrix':covar,'title':name,'parmDict':parmDict} # SeqResult['histNames'] = Names # G2frame.GPXtree.SetItemPyData(Id,SeqResult) else: wx.BeginBusyCursor() finally: dlg.Destroy() wx.EndBusyCursor() # print ('All selected images recalibrated - results in Sequential image calibration results') # G2frame.G2plotNB.Delete('Sequential refinement') #clear away probably invalid plot # G2plt.PlotExposedImage(G2frame,event=None) # G2frame.GPXtree.SelectItem(Id) def OnClearCalib(event): data['ring'] = [] data['rings'] = [] data['ellipses'] = [] G2plt.PlotExposedImage(G2frame,event=event) def ResetThresholds(): Imin = max(0.,np.min(G2frame.ImageZ)) Imax = np.max(G2frame.ImageZ) data['range'] = [(0,Imax),[Imin,Imax]] masks['Thresholds'] = [(0,Imax),[Imin,Imax]] G2frame.slideSizer.GetChildren()[1].Window.SetValue(Imax) #tricky G2frame.slideSizer.GetChildren()[4].Window.SetValue(Imin) #tricky def OnIntegrate(event,useTA=None,useMask=None): '''Integrate image in response to a menu event or from the AutoIntegrate dialog. In the latter case, event=None. ''' CleanupMasks(masks) sumImg = GetImageZ(G2frame,data) if not masks.get('SpotMask',{'spotMask':None})['spotMask'] is None: sumImg = ma.array(sumImg,mask=masks['SpotMask']['spotMask']) G2frame.Integrate = G2img.ImageIntegrate(sumImg,data,masks,blkSize,useTA=useTA,useMask=useMask) G2frame.PauseIntegration = G2frame.Integrate[-1] del sumImg #force cleanup Id = G2IO.SaveIntegration(G2frame,G2frame.PickId,data,(event is None)) G2frame.PatternId = Id G2frame.GPXtree.SelectItem(Id) G2frame.GPXtree.Expand(Id) for item in G2frame.MakePDF: item.Enable(True) def OnIntegrateAll(event): Names = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',]) dlg = G2G.G2MultiChoiceDialog(G2frame,'Image integration controls','Select images to integrate:',Names) try: if dlg.ShowModal() == wx.ID_OK: items = dlg.GetSelections() G2frame.EnablePlot = False dlgp = wx.ProgressDialog("Elapsed time","2D image integrations",len(items)+1, style = wx.PD_ELAPSED_TIME|wx.PD_CAN_ABORT) try: pId = 0 oldData = {'tilt':0.,'distance':0.,'rotation':0.,'center':[0.,0.],'DetDepth':0.,'azmthOff':0.,'det2theta':0.} oldMhash = 0 for icnt,item in enumerate(items): dlgp.Raise() GoOn = dlgp.Update(icnt) if not GoOn[0]: break name = Names[item] G2frame.Image = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,name) CId = G2gd.GetGPXtreeItemId(G2frame,G2frame.Image,'Image Controls') Data = G2frame.GPXtree.GetItemPyData(CId) same = True for item in ['tilt','distance','rotation','DetDepth','azmthOff','det2theta']: if Data[item] != oldData[item]: same = False if (Data['center'][0] != oldData['center'][0] or Data['center'][1] != oldData['center'][1]): same = False if not same: t0 = time.time() useTA = G2img.MakeUseTA(Data,blkSize) print(' Use new image controls; new xy -> th,azm time %.3f'%(time.time()-t0)) Masks = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.Image,'Masks')) Mhash = copy.deepcopy(Masks) Mhash.pop('Thresholds') Mhash = hash(str(Mhash)) if Mhash != oldMhash: t0 = time.time() useMask = G2img.MakeUseMask(Data,Masks,blkSize) print(' Use new mask; make mask time: %.3f'%(time.time()-t0)) oldMhash = Mhash image = GetImageZ(G2frame,Data) if not Masks['SpotMask']['spotMask'] is None: image = ma.array(image,mask=Masks['SpotMask']['spotMask']) G2frame.Integrate = G2img.ImageIntegrate(image,Data,Masks,blkSize,useTA=useTA,useMask=useMask) del image #force cleanup pId = G2IO.SaveIntegration(G2frame,CId,Data) oldData = Data finally: dlgp.Destroy() G2frame.EnablePlot = True if pId: G2frame.GPXtree.SelectItem(pId) G2frame.GPXtree.Expand(pId) G2frame.PatternId = pId finally: dlg.Destroy() def OnCopyControls(event): Names = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',]) if len(Names) == 1: G2frame.ErrorDialog('Nothing to copy controls to','There must be more than one "IMG" pattern') return Source = G2frame.GPXtree.GetItemText(G2frame.Image) Names.pop(Names.index(Source)) # select targets & do copy dlg = G2G.G2MultiChoiceDialog(G2frame,'Copy image controls','Copy controls from '+Source+' to:',Names) try: if dlg.ShowModal() == wx.ID_OK: items = dlg.GetSelections() G2frame.EnablePlot = False for item in items: #preserve some values name = Names[item] Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,name) CId = G2gd.GetGPXtreeItemId(G2frame,Id,'Image Controls') oldData = copy.deepcopy(G2frame.GPXtree.GetItemPyData(CId)) Data = copy.deepcopy(data) Data['range'][0] = oldData['range'][0] Data['size'] = oldData['size'] Data['GonioAngles'] = oldData.get('GonioAngles', [0.,0.,0.]) Data['samplechangerpos'] = oldData.get('samplechangerpos',0.0) Data['det2theta'] = oldData.get('det2theta',0.0) Data['ring'] = [] Data['rings'] = [] Data['ellipses'] = [] if name == Data['dark image'][0]: Data['dark image'] = ['',-1.] if name == Data['background image'][0]: Data['background image'] = ['',-1.] G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Image Controls'),Data) finally: dlg.Destroy() if G2frame.PickId: G2frame.GPXtree.SelectItem(G2frame.PickId) def OnCopySelected(event): Names = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',]) if len(Names) == 1: G2frame.ErrorDialog('Nothing to copy controls to','There must be more than one "IMG" pattern') return Source = G2frame.GPXtree.GetItemText(G2frame.Image) # Assemble a list of item labels keyList = ['type','color','wavelength','calibrant','distance','center','Oblique', 'tilt','rotation','azmthOff','fullIntegrate','LRazimuth','setdist', 'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth', 'calibskip','pixLimit','cutoff','calibdmin','Flat Bkg','varyList','orientation', 'binType','SampleShape','PolaVal','SampleAbs','dark image','background image'] keyList.sort(key=lambda s: s.lower()) keyText = [i+' = '+str(data[i]) for i in keyList] # sort both lists together, ordered by keyText selectedKeys = [] dlg = G2G.G2MultiChoiceDialog(G2frame,'Select which image controls\nto copy', 'Select image controls', keyText) try: if dlg.ShowModal() == wx.ID_OK: selectedKeys = [keyList[i] for i in dlg.GetSelections()] finally: dlg.Destroy() if not selectedKeys: return # nothing to copy copyDict = {} for parm in selectedKeys: copyDict[parm] = data[parm] dlg = G2G.G2MultiChoiceDialog(G2frame,'Copy image controls from\n'+Source+' to...', 'Copy image controls', Names) try: if dlg.ShowModal() == wx.ID_OK: result = dlg.GetSelections() for i in result: item = Names[i] Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item) Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Image Controls')) Controls.update(copy.deepcopy(copyDict)) finally: dlg.Destroy() def OnSaveControls(event): pth = G2G.GetExportPath(G2frame) dlg = wx.FileDialog(G2frame, 'Choose image controls file', pth, '', 'image control files (*.imctrl)|*.imctrl',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT) try: if dlg.ShowModal() == wx.ID_OK: filename = dlg.GetPath() # make sure extension is .imctrl filename = os.path.splitext(filename)[0]+'.imctrl' G2fil.WriteControls(filename,data) finally: dlg.Destroy() def OnSaveMultiControls(event): '''Save controls from multiple images ''' imglist = [] item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root) while item: name = G2frame.GPXtree.GetItemText(item) if name.startswith('IMG '): imglist.append(name) item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie) if not imglist: print('No images!') return dlg = G2G.G2MultiChoiceDialog(G2frame, 'Which images to select?', 'Select images', imglist, wx.CHOICEDLG_STYLE) try: if dlg.ShowModal() == wx.ID_OK: treeEntries = [imglist[i] for i in dlg.GetSelections()] finally: dlg.Destroy() if not treeEntries: print('No images selected!') return pth = G2G.GetExportPath(G2frame) dlg = wx.DirDialog( G2frame, 'Select directory for output files',pth,wx.DD_DEFAULT_STYLE) dlg.CenterOnParent() outdir = None try: if dlg.ShowModal() == wx.ID_OK: outdir = dlg.GetPath() finally: dlg.Destroy() if not outdir: print('No directory') return for img in treeEntries: item = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,img) data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId( G2frame,item,'Image Controls')) Npix,imagefile,imagetag = G2frame.GPXtree.GetImageLoc(item) filename = os.path.join(outdir, os.path.splitext(os.path.split(imagefile)[1])[0] + '.imctrl') print('writing '+filename) G2fil.WriteControls(filename,data) def OnLoadControls(event): pth = G2G.GetImportPath(G2frame) if not pth: pth = '.' dlg = wx.FileDialog(G2frame, 'Choose image controls file', pth, '', 'image control files (*.imctrl)|*.imctrl',wx.FD_OPEN) try: if dlg.ShowModal() == wx.ID_OK: filename = dlg.GetPath() File = open(filename,'r') Slines = File.readlines() File.close() G2fil.LoadControls(Slines,data) finally: dlg.Destroy() G2frame.ImageZ = GetImageZ(G2frame,data) ResetThresholds() G2plt.PlotExposedImage(G2frame,event=event) wx.CallLater(100,UpdateImageControls,G2frame,data,masks) def OnLoadMultiControls(event): #TODO: how read in multiple image controls & match them by 'twoth' tag? print('This is not implemented yet, sorry') G2G.G2MessageBox(G2frame,'This is not implemented yet, sorry') return pth = G2G.GetImportPath(G2frame) if not pth: pth = '.' controlsDict = {} dlg = wx.FileDialog(G2frame, 'Choose image control files', pth, '', 'image control files (*.imctrl)|*.imctrl',wx.FD_OPEN|wx.FD_MULTIPLE) try: if dlg.ShowModal() == wx.ID_OK: filelist = dlg.GetPaths() if len(filelist) == 0: return for filename in filelist: File = open(filename,'r') Slines = File.readlines() for S in Slines: if S.find('twoth') == 0: indx = S.split(':')[1][:-1] #remove '\n'! controlsDict[indx] = Slines File.close() finally: dlg.Destroy() if not len(controlsDict): return Names = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',]) dlg = G2G.G2MultiChoiceDialog(G2frame,'Select images','Select images for updating controls:', Names) try: if dlg.ShowModal() == wx.ID_OK: images = dlg.GetSelections() if not len(images): return for image in images: Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Names[image]) imctrls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Image Controls')) Slines = controlsDict[imctrls['twoth']] G2fil.LoadControls(Slines,imctrls) finally: dlg.Destroy() def OnTransferAngles(event): '''Sets the integration range for the selected Images based on the difference in detector distance ''' Names = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',]) if len(Names) == 1: G2frame.ErrorDialog('No images to transfer integration angles to','Need more "IMG"s') return Source = G2frame.GPXtree.GetItemText(G2frame.Image) Names.pop(Names.index(Source)) # select targets & do copy extraopts = {"label_1":"Xfer scaled calib d-min", "value_1":False, "label_2":"Xfer scaled 2-theta min", "value_2":False, "label_3":"Xfer scaled 2-theta max", "value_3":True, "label_4":"Xfer fixed background ", "value_4":False, } dlg = G2G.G2MultiChoiceDialog(G2frame,'Xfer angles','Transfer integration range from '+Source+' to:', Names,extraOpts=extraopts) try: if dlg.ShowModal() == wx.ID_OK: for i in '_1','_2','_3','_4': if extraopts['value'+i]: break else: G2G.G2MessageBox(G2frame,'Nothing to do!') return xferAng = lambda tth,dist1,dist2: atand(dist1 * tand(tth) / dist2) items = dlg.GetSelections() G2frame.EnablePlot = False Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Source) data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Image Controls')) ttmin0,ttmax0 = data['IOtth'] dist0 = data['distance'] wave0 = data['wavelength'] dsp0 = data['calibdmin'] flatBkg = data['Flat Bkg'] print('distance = {:.2f} integration range: [{:.4f}, {:.4f}], calib dmin {:.3f}' .format(dist0,ttmin0,ttmax0,dsp0)) for item in items: name = Names[item] Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,name) data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Image Controls')) dist1 = data['distance'] if extraopts["value_2"]: data['IOtth'][0] = xferAng(ttmin0,dist0,dist1) if extraopts["value_3"]: data['IOtth'][1] = xferAng(ttmax0,dist0,dist1) if extraopts["value_1"]: ang1 = xferAng(2.0*asind(wave0/(2.*dsp0)),dist0,dist1) data['calibdmin'] = data['wavelength']/(2.*sind(ang1/2.)) print('distance = {:.2f} integration range: [{:.4f}, {:.4f}], calib dmin {:.3f}' .format(dist1,data['IOtth'][0],data['IOtth'][1],data['calibdmin'])) if extraopts['value_4']: data['Flat Bkg'] = flatBkg*(dist0/dist1)**2 else: print('distance = {:.2f} integration range: [{:.4f}, {:.4f}]' .format(dist1,data['IOtth'][0],data['IOtth'][1])) finally: dlg.Destroy() G2frame.GPXtree.SelectItem(G2frame.PickId) def OnResetDist(event): dlg = wx.MessageDialog(G2frame,'Are you sure you want to do this?',caption='Reset dist to set dist',style=wx.YES_NO|wx.ICON_EXCLAMATION) if dlg.ShowModal() != wx.ID_YES: dlg.Destroy() return dlg.Destroy() Names = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',]) dlg = G2G.G2MultiChoiceDialog(G2frame,'Reset dist','Reset dist to set dist for:',Names) try: if dlg.ShowModal() == wx.ID_OK: items = dlg.GetSelections() for item in items: name = Names[item] Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,name) Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Image Controls')) Data['distance'] = Data['setdist'] finally: dlg.Destroy() wx.CallAfter(UpdateImageControls,G2frame,data,masks) # Sizers Indx = {} def ComboSizer(): def OnDataType(event): data['type'] = typeSel.GetValue()[:4] if 'SASD' in data['type']: data['SampleAbs'][0] = np.exp(-data['SampleAbs'][0]) #switch from muT to trans! if data['binType'] == '2-theta': data['binType'] = 'log(q)' #switch default bin type elif 'PWDR' in data['type']: data['SampleAbs'][0] = -np.log(data['SampleAbs'][0]) #switch from trans to muT! if data['binType'] == 'log(q)': data['binType'] = '2-theta' #switch default bin type wx.CallLater(100,UpdateImageControls,G2frame,data,masks) def OnNewColorBar(event): data['color'] = colSel.GetValue() wx.CallAfter(G2plt.PlotExposedImage,G2frame,event=event) def OnAzmthOff(invalid,value,tc): wx.CallAfter(G2plt.PlotExposedImage,G2frame,event=tc.event) comboSizer = wx.BoxSizer(wx.HORIZONTAL) comboSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Type of image data: '),0,WACV) typeSel = wx.ComboBox(parent=G2frame.dataWindow,value=typeDict[data['type']],choices=typeList, style=wx.CB_READONLY|wx.CB_DROPDOWN) typeSel.SetValue(data['type']) typeSel.Bind(wx.EVT_COMBOBOX, OnDataType) comboSizer.Add(typeSel,0,WACV) comboSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Color bar '),0,WACV) colSel = wx.ComboBox(parent=G2frame.dataWindow,value=data['color'],choices=colorList, style=wx.CB_READONLY|wx.CB_DROPDOWN) colSel.Bind(wx.EVT_COMBOBOX, OnNewColorBar) comboSizer.Add(colSel,0,WACV) comboSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Azimuth offset '),0,WACV) azmthOff = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'azmthOff',nDig=(10,2), typeHint=float,OnLeave=OnAzmthOff) comboSizer.Add(azmthOff,0,WACV) return comboSizer def MaxSizer(): '''Defines a sizer with sliders and TextCtrl widgets for controlling the colormap for the image, as well as callback routines. ''' def OnNewVal(invalid,value,tc): '''Called when a Imax or Imin value is typed into a Validated TextCrtl (which puts the value into the data['range'] nested list). This adjusts the slider positions to match the current values ''' scaleSel.SetSelection(len(scaleChoices)-1) r11 = min(max(Range[1][1],Range[1][0]+1),Range[0][1]) # keep values in range if r11 != Range[1][1]: Range[1][1] = r11 maxVal.SetValue(int(Range[1][1])) r10 = max(min(Range[1][0],Range[1][1]-1),Range[0][0]) if r10 != Range[1][0]: Range[1][0] = r10 minVal.SetValue(int(Range[1][0])) sqrtDeltZero = math.sqrt(max(1.0,Range[0][1]-max(0.0,Range[1][0])-1)) # sqrt(Imax0-Imin-1) sqrtDeltOne = math.sqrt(max(1.0,Range[1][1]-max(0.0,Range[1][0])-1)) # sqrt(Imax-Imin-1) sv1 = min(100,max(0,int(0.5+100.*sqrtDeltOne/sqrtDeltZero))) maxSel.SetValue(sv1) DeltOne = max(1.0,Range[1][1]-max(0.0,Range[0][0])-1) sv0 = min(100,max(0,int(0.5+100.*(Range[1][0]-Range[0][0])/DeltOne))) minSel.SetValue(sv0) new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('2D Powder Image','mpl',newImage=False) Page.ImgObj.set_clim([Range[1][0],Range[1][1]]) if mplOld: Page.canvas.draw() else: Page.canvas.draw_idle() G2frame.prevMaxValue = None def OnMaxSlider(event): val = maxSel.GetValue() if G2frame.prevMaxValue == val: return # if this val has been processed, no need to repeat scaleSel.SetSelection(len(scaleChoices)-1) G2frame.prevMaxValue = val sqrtDeltZero = math.sqrt(max(1.0,Range[0][1]-max(0.0,Range[1][0])-1)) # sqrt(Imax0-Imin-1) Range[1][1] = int(0.5 + (val * sqrtDeltZero / 100.)**2 + Range[1][0] + 1) maxVal.SetValue(int(0.5+Range[1][1])) DeltOne = max(1.0,Range[1][1]-max(0.0,Range[0][0])-1) minSel.SetValue(int(0.5 + 100*(Range[1][0]/DeltOne))) sv0 = min(100,max(0,int(0.5+100.*(Range[1][0]-Range[0][0])/DeltOne))) minSel.SetValue(sv0) new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('2D Powder Image','mpl',newImage=False) Page.ImgObj.set_clim([Range[1][0],Range[1][1]]) if mplOld: Page.canvas.draw() else: Page.canvas.draw_idle() G2frame.prevMinValue = None def OnMinSlider(event): val = minSel.GetValue() scaleSel.SetSelection(len(scaleChoices)-1) if G2frame.prevMinValue == val: return # if this val has been processed, no need to repeat G2frame.prevMinValue = val DeltOne = max(1.0,Range[1][1]-max(0.0,Range[0][0])-1) # Imax-Imin0-1 Range[1][0] = max(0,int(0.5 + val * DeltOne / 100 + Range[0][0])) minVal.SetValue(int(Range[1][0])) sqrtDeltZero = math.sqrt(max(1.0,Range[0][1]-max(0.0,Range[1][0])-1)) # sqrt(Imax0-Imin-1) sqrtDeltOne = math.sqrt(max(1.0,Range[1][1]-max(0.0,Range[1][0])-1)) # sqrt(Imax-Imin-1) sv1 = min(100,max(0,int(0.5+100.*sqrtDeltOne/sqrtDeltZero))) maxSel.SetValue(sv1) new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('2D Powder Image','mpl',newImage=False) Page.ImgObj.set_clim([Range[1][0],Range[1][1]]) if mplOld: Page.canvas.draw() else: Page.canvas.draw_idle() def OnAutoSet(event): '''Responds to a button labeled 95%, etc; Sets the Imax and Imin values for the image so that 95% (etc.) of pixels are inside the color map limits. An equal number of pixels are dropped at the minimum and maximum levels. ''' try: val = int(event.GetEventObject().GetStringSelection()[:-1]) margin = (100-val)/2. except: margin = 0 event.GetEventObject().SetSelection(0) new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('2D Powder Image','mpl',newImage=False) if margin == 0: Range[1] = list(Range[0]) else: Range[1][0] = int(np.percentile(Page.ImgObj.get_array().compressed(),margin)) Range[1][1] = int(np.percentile(Page.ImgObj.get_array().compressed(),100-margin)) sqrtDeltZero = math.sqrt(max(1.0,Range[0][1]-max(0.0,Range[1][0])-1)) # sqrt(Imax0-Imin-1) sqrtDeltOne = math.sqrt(max(1.0,Range[1][1]-max(0.0,Range[1][0])-1)) # sqrt(Imax-Imin-1) sv1 = min(100,max(0,int(0.5+100.*sqrtDeltOne/sqrtDeltZero))) maxSel.SetValue(sv1) DeltOne = max(1.0,Range[1][1]-max(0.0,Range[0][0])-1) sv0 = min(100,max(0,int(0.5+100.*(Range[1][0]-Range[0][0])/DeltOne))) minSel.SetValue(sv0) minVal.SetValue(int(Range[1][0])) maxVal.SetValue(int(Range[1][1])) new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('2D Powder Image','mpl',newImage=False) Page.ImgObj.set_clim([Range[1][0],Range[1][1]]) if mplOld: Page.canvas.draw() else: Page.canvas.draw_idle() def OnLineScan(event): data['linescan'][0] = linescan.GetValue() wx.CallAfter(UpdateImageControls,G2frame,data,masks) G2plt.PlotExposedImage(G2frame,event=event) def OnNewLineScan(invalid,value,tc): G2plt.PlotExposedImage(G2frame,event=None) def OnMoveAzm(event): data['linescan'][1] += float(azmSpin.GetValue()) data['linescan'][1] = data['linescan'][1]%360. G2frame.scanazm.SetValue(data['linescan'][1]) G2plt.PlotExposedImage(G2frame,event=event) mplv = mpl.__version__.split('.') mplOld = mplv[0] == '1' and int(mplv[1]) < 4 # use draw_idle for newer matplotlib versions # Plot color scaling uses limits as below: # (Imin0, Imax0) => Range[0] = data['range'][0] # lowest to highest pixel intensity # [Imin, Imax] => Range[1] = data['range'][1] # lowest to highest pixel intensity on cmap scale maxSizer = wx.BoxSizer(wx.VERTICAL) G2frame.slideSizer = wx.FlexGridSizer(2,3,5,5) G2frame.slideSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Max intensity'),0,WACV) # maxSel is a slider with 101 steps scaled from Imin+1 to Imax0 with sqrt scaling # slider value = sv = 100 * sqrt((Imax-Imin-1)/(Imax0-Imin-1)) # Imax = (sv * sqrt(Imax0-Imin-1) / 100)**2 + Imin + 1 sqrtDeltZero = math.sqrt(max(1.0,Range[0][1]-max(0.0,Range[1][0])-1)) # sqrt(Imax0-Imin-1) sqrtDeltOne = math.sqrt(max(1.0,Range[1][1]-max(0.0,Range[1][0])-1)) # sqrt(Imax-Imin-1) sv1 = min(100,max(0,int(0.5+100.*sqrtDeltOne/sqrtDeltZero))) maxSel = wx.Slider(parent=G2frame.dataWindow,style=wx.SL_HORIZONTAL,value=sv1) G2frame.slideSizer.AddGrowableCol(2) maxSel.Bind(wx.EVT_SLIDER, OnMaxSlider) maxVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,Range[1],1,xmin=Range[0][0]+1, xmax=Range[0][1],OnLeave=OnNewVal) G2frame.slideSizer.Add(maxVal,0,WACV) G2frame.slideSizer.Add(maxSel,flag=wx.EXPAND|wx.ALL) G2frame.slideSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Min intensity'),0,WACV) # minSel is a slider with 101 steps scaled from Imin0 to Imax-1 with linear scaling # slider value = sv0 = 100 * (Imin-Imin0)/(Imax-Imin0-1) # Imin = sv0 * (Imax-Imin0-1) / 100 + Imin0 DeltOne = max(1.0,Range[1][1]-max(0.0,Range[0][0])-1) # Imax-Imin0-1 sv0 = min(100,max(0,int(0.5+100.*(Range[1][0]-Range[0][0])/DeltOne))) minSel = wx.Slider(parent=G2frame.dataWindow,style=wx.SL_HORIZONTAL,value=sv0) minSel.Bind(wx.EVT_SLIDER, OnMinSlider) minVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,Range[1],0, xmax=Range[0][1],typeHint=int,OnLeave=OnNewVal) G2frame.slideSizer.Add(minVal,0,WACV) G2frame.slideSizer.Add(minSel,flag=wx.EXPAND|wx.ALL) maxSizer.Add(G2frame.slideSizer,flag=wx.EXPAND|wx.ALL) autoSizer = wx.BoxSizer(wx.HORIZONTAL) autoSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Auto scaler '),0,WACV) scaleChoices = ("100%","99%","95%","90%","80%","?") scaleSel = wx.Choice(G2frame.dataWindow,choices=scaleChoices,size=(-1,-1)) if (Range[1][0] == Range[0][0] and Range[1][1] == Range[0][1]): scaleSel.SetSelection(0) else: scaleSel.SetSelection(len(scaleChoices)-1) scaleSel.Bind(wx.EVT_CHOICE,OnAutoSet) autoSizer.Add(scaleSel,0,WACV) if data['linescan'][0]: linescan = wx.CheckBox(G2frame.dataWindow,label=' Show line scan at azm = ') else: linescan = wx.CheckBox(G2frame.dataWindow,label=' Show line scan') linescan.Bind(wx.EVT_CHECKBOX,OnLineScan) linescan.SetValue(data['linescan'][0]) autoSizer.Add((5,0),0) autoSizer.Add(linescan,0,WACV) if data['linescan'][0]: G2frame.scanazm = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['linescan'],1,xmin=0., xmax=360.,OnLeave=OnNewLineScan) autoSizer.Add(G2frame.scanazm,0,WACV) azmSpin = wx.SpinButton(G2frame.dataWindow,style=wx.SP_VERTICAL,size=wx.Size(20,25)) azmSpin.SetValue(0) azmSpin.SetRange(-1,1) azmSpin.Bind(wx.EVT_SPIN, OnMoveAzm) autoSizer.Add(azmSpin,0,WACV) maxSizer.Add(autoSizer) return maxSizer def CalibCoeffSizer(): def OnCalRef(event): Obj = event.GetEventObject() name = Indx[Obj] data['varyList'][name] = Obj.GetValue() calibSizer = wx.FlexGridSizer(0,2,5,5) calibSizer.SetFlexibleDirection(wx.HORIZONTAL) calibSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Calibration coefficients'),0,WACV) calibSizer.Add((5,0),0) Names = ['det-X','det-Y','wave','dist','tilt','phi'] if 'PWDR' in data['type']: Names.append('dep') Parms = {'dist':['Distance',(10,3),data,'distance'],'det-X':['Beam center X',(10,3),data['center'],0], 'det-Y':['Beam center Y',(10,3),data['center'],1],'tilt':['Tilt angle*',(10,3),data,'tilt'], 'phi':['Tilt rotation*',(10,2),data,'rotation'],'dep':['Penetration*',(10,4),data,'DetDepth'], 'wave':['Wavelength*',(10,6),data,'wavelength']} for name in Names: calSel = wx.CheckBox(parent=G2frame.dataWindow,label=Parms[name][0]) calibSizer.Add(calSel,0,WACV) calSel.Bind(wx.EVT_CHECKBOX, OnCalRef) calSel.SetValue(data['varyList'][name]) Indx[calSel] = name if name == 'wave': calVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,Parms[name][2], Parms[name][3],xmin=0.01,xmax=10.,nDig=Parms[name][1],typeHint=float) elif name == 'dep': calVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,Parms[name][2], Parms[name][3],xmin=0.0,xmax=0.2,nDig=Parms[name][1],typeHint=float) else: calVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,Parms[name][2], Parms[name][3],nDig=Parms[name][1],typeHint=float) calibSizer.Add(calVal,0,WACV) return calibSizer def IntegrateSizer(): def OnNewBinType(event): data['binType'] = binSel.GetValue() wx.CallLater(100,UpdateImageControls,G2frame,data,masks) def OnIOtth(invalid,value,tc): Ltth = float(G2frame.InnerTth.GetValue()) Utth = float(G2frame.OuterTth.GetValue()) if Ltth > Utth: Ltth,Utth = Utth,Ltth if 'q' in data['binType'].lower(): data['IOtth'] = [2.*asind(Ltth*wave/(4.*math.pi)),2.*asind(Utth*wave/(4.*math.pi))] else: data['IOtth'] = [Ltth,Utth] G2frame.InnerTth.SetValue(Ltth) G2frame.OuterTth.SetValue(Utth) wx.CallAfter(G2plt.PlotExposedImage,G2frame,event=tc.event) def OnLRazim(invalid,value,tc): Lazm = float(G2frame.Lazim.GetValue())%360. Razm = float(G2frame.Razim.GetValue())%360. if Lazm > Razm: Razm += 360. if data['fullIntegrate']: Razm = Lazm+360. G2frame.Lazim.SetValue(Lazm) G2frame.Razim.SetValue(Razm) data['LRazimuth'] = [Lazm,Razm] wx.CallAfter(G2plt.PlotExposedImage,G2frame,event=tc.event) def OnNumOutAzms(invalid,value,tc): wx.CallAfter(G2plt.PlotExposedImage,G2frame,event=tc.event) def OnNumOutBins(invalid,value,tc): data['outChannels'] = (data['outChannels']//4)*4 outChan.SetValue(data['outChannels']) def OnOblique(event): data['Oblique'][1] = not data['Oblique'][1] def OnSampleShape(event): data['SampleShape'] = samShape.GetValue() if 'Cylind' in data['SampleShape']: data['SampleAbs'][0] = 0.0 elif 'Fixed' in data['SampleShape']: data['SampleAbs'][0] = 1.0 wx.CallLater(100,UpdateImageControls,G2frame,data,masks) def OnSamAbs(event): data['SampleAbs'][1] = not data['SampleAbs'][1] wx.CallLater(100,UpdateImageControls,G2frame,data,masks) def OnShowLines(event): data['showLines'] = not data['showLines'] G2plt.PlotExposedImage(G2frame,event=event) def OnFullIntegrate(event): Lazm = float(G2frame.Lazim.GetValue()) if data['fullIntegrate']: data['fullIntegrate'] = False data['LRazimuth'] = [Lazm,Lazm+20.] else: data['fullIntegrate'] = True data['LRazimuth'] = [Lazm,Lazm+360.] wx.CallLater(100,UpdateImageControls,G2frame,data,masks) G2plt.PlotExposedImage(G2frame,event=event) def OnSetDefault(event): if data['setDefault']: G2frame.imageDefault = {} data['setDefault'] = False else: G2frame.imageDefault = copy.deepcopy(data) G2frame.imageDefault['setDefault'] = False if 'formatName' in G2frame.imageDefault: del G2frame.imageDefault['formatName'] data['setDefault'] = True def OnCenterAzm(event): data['centerAzm'] = not data['centerAzm'] wx.CallAfter(G2plt.PlotExposedImage,G2frame,event=event) def OnApplyPola(event): data['PolaVal'][1] = not data['PolaVal'][1] def OnIfPink(event): data['IfPink'] = not data['IfPink'] def OnOchoice(event): data['orientation'] = ochoice.GetValue() dataSizer = wx.FlexGridSizer(0,2,5,3) dataSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Integration coefficients'),0,WACV) dataSizer.Add((5,0),0) if 'PWDR' in data['type']: binChoice = ['2-theta','Q'] elif 'SASD' in data['type']: binChoice = ['2-theta','Q','log(q)'] dataSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Bin style: Constant step bins in'),0,WACV) littleSizer = wx.BoxSizer(wx.HORIZONTAL) binSel = wx.ComboBox(G2frame.dataWindow,value=data['binType'],choices=binChoice, style=wx.CB_READONLY|wx.CB_DROPDOWN) binSel.Bind(wx.EVT_COMBOBOX, OnNewBinType) littleSizer.Add(binSel,0,WACV) pinkSel = wx.CheckBox(G2frame.dataWindow,label=' Pink beam source?') pinkSel.SetValue(data['IfPink']) pinkSel.Bind(wx.EVT_CHECKBOX,OnIfPink) littleSizer.Add(pinkSel,0,WACV) dataSizer.Add(littleSizer) binType = '2-theta' if 'q' in data['binType'].lower(): binType = 'Q' dataSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Inner/Outer '+binType),0,WACV) IOtth = data['IOtth'][:] if 'q' in data['binType'].lower(): wave = data['wavelength'] IOtth = [4.*math.pi*sind(IOtth[0]/2.)/wave,4.*math.pi*sind(IOtth[1]/2.)/wave] littleSizer = wx.BoxSizer(wx.HORIZONTAL) G2frame.InnerTth = G2G.ValidatedTxtCtrl(G2frame.dataWindow,IOtth,0,nDig=(8,3,'f'),xmin=0.001,typeHint=float,OnLeave=OnIOtth) littleSizer.Add(G2frame.InnerTth,0,WACV) G2frame.OuterTth = G2G.ValidatedTxtCtrl(G2frame.dataWindow,IOtth,1,nDig=(8,3,'f'),xmin=0.001,typeHint=float,OnLeave=OnIOtth) littleSizer.Add(G2frame.OuterTth,0,WACV) dataSizer.Add(littleSizer,0,) dataSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Start/End azimuth'),0,WACV) LRazim = data['LRazimuth'] littleSizer = wx.BoxSizer(wx.HORIZONTAL) G2frame.Lazim = G2G.ValidatedTxtCtrl(G2frame.dataWindow,LRazim,0,nDig=(6,1,'f'),typeHint=float,OnLeave=OnLRazim) littleSizer.Add(G2frame.Lazim,0,WACV) G2frame.Razim = G2G.ValidatedTxtCtrl(G2frame.dataWindow,LRazim,1,nDig=(6,1,'f'),typeHint=float,OnLeave=OnLRazim) if data['fullIntegrate']: G2frame.Razim.Enable(False) G2frame.Razim.SetBackgroundColour(VERY_LIGHT_GREY) G2frame.Razim.SetValue(LRazim[0]+360.) littleSizer.Add(G2frame.Razim,0,WACV) dataSizer.Add(littleSizer,0,) dataSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' No. 2-theta/azimuth bins'),0,WACV) littleSizer = wx.BoxSizer(wx.HORIZONTAL) outChan = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'outChannels',typeHint=int,xmin=10,OnLeave=OnNumOutBins) littleSizer.Add(outChan,0,WACV) outAzim = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'outAzimuths',nDig=(10,4),xmin=1,typeHint=int,OnLeave=OnNumOutAzms) littleSizer.Add(outAzim,0,WACV) dataSizer.Add(littleSizer) showLines = wx.CheckBox(parent=G2frame.dataWindow,label='Show integration limits?') dataSizer.Add(showLines,0,WACV) showLines.Bind(wx.EVT_CHECKBOX, OnShowLines) showLines.SetValue(data['showLines']) fullIntegrate = wx.CheckBox(parent=G2frame.dataWindow,label='Do full integration?') dataSizer.Add(fullIntegrate,0,WACV) fullIntegrate.Bind(wx.EVT_CHECKBOX, OnFullIntegrate) fullIntegrate.SetValue(data['fullIntegrate']) setDefault = wx.CheckBox(parent=G2frame.dataWindow,label='Use for all new images?') dataSizer.Add(setDefault,0,WACV) setDefault.Bind(wx.EVT_CHECKBOX, OnSetDefault) setDefault.SetValue(data['setDefault']) centerAzm = wx.CheckBox(parent=G2frame.dataWindow,label='Azimuth at bin center?') dataSizer.Add(centerAzm,0,WACV) centerAzm.Bind(wx.EVT_CHECKBOX, OnCenterAzm) centerAzm.SetValue(data['centerAzm']) #SampleShape - cylinder or flat plate choice? littleSizer = wx.BoxSizer(wx.HORIZONTAL) samabs = wx.CheckBox(parent=G2frame.dataWindow,label='Apply sample absorption?') dataSizer.Add(samabs,0,WACV) samabs.Bind(wx.EVT_CHECKBOX, OnSamAbs) samabs.SetValue(data['SampleAbs'][1]) minmax = [0.,2.] if data['SampleAbs'][1]: samplechoice = ['Cylinder','Fixed flat plate',] littleSizer.Add(wx.StaticText(G2frame.dataWindow,label='Select shape '),0,WACV) samShape = wx.ComboBox(G2frame.dataWindow,value=data['SampleShape'],choices=samplechoice, style=wx.CB_READONLY|wx.CB_DROPDOWN) samShape.Bind(wx.EVT_COMBOBOX,OnSampleShape) littleSizer.Add(samShape,0,WACV) dataSizer.Add(littleSizer) if data['SampleAbs'][1]: littleSizer = wx.BoxSizer(wx.HORIZONTAL) if 'Cylind' in data['SampleShape']: #cylinder mu*R; flat plate transmission littleSizer.Add(wx.StaticText(G2frame.dataWindow,label='mu*R (0.00-2.0) '),0,WACV) elif 'Fixed' in data['SampleShape']: littleSizer.Add(wx.StaticText(G2frame.dataWindow,label='transmission '),0,WACV) #for flat plate minmax = [.05,1.0] samabsVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['SampleAbs'],0,nDig=(10,3), typeHint=float,xmin=minmax[0],xmax=minmax[1]) littleSizer.Add(samabsVal,0,WACV) dataSizer.Add(littleSizer,0,WACV) if 'Cylind' in data['SampleShape'] and data['SampleAbs'][1]: littleSizer = wx.BoxSizer(wx.HORIZONTAL) littleSizer.Add(wx.StaticText(G2frame.dataWindow,label='Select orientation '),0,WACV) choice = ['horizontal','vertical'] ochoice = wx.ComboBox(G2frame.dataWindow,value=data['orientation'],choices=choice, style=wx.CB_READONLY|wx.CB_DROPDOWN) ochoice.Bind(wx.EVT_COMBOBOX,OnOchoice) littleSizer.Add(ochoice,0,WACV) dataSizer.Add(littleSizer) if 'flat' in data['SampleShape'] and data['SampleAbs'][1]: dataSizer.Add((5,5),0) if 'PWDR' in data['type']: littleSizer = wx.BoxSizer(wx.HORIZONTAL) oblique = wx.CheckBox(parent=G2frame.dataWindow,label='Apply detector absorption?') dataSizer.Add(oblique,0,WACV) oblique.Bind(wx.EVT_CHECKBOX, OnOblique) oblique.SetValue(data['Oblique'][1]) littleSizer.Add(wx.StaticText(G2frame.dataWindow,label='Value (0.01-0.99) '),0,WACV) obliqVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Oblique'],0,nDig=(10,3),typeHint=float,xmin=0.01,xmax=0.99) littleSizer.Add(obliqVal,0,WACV) dataSizer.Add(littleSizer,0,) if 'SASD' in data['type']: littleSizer = wx.BoxSizer(wx.HORIZONTAL) setPolariz = wx.CheckBox(parent=G2frame.dataWindow,label='Apply polarization?') dataSizer.Add(setPolariz,0,WACV) setPolariz.Bind(wx.EVT_CHECKBOX, OnApplyPola) setPolariz.SetValue(data['PolaVal'][1]) littleSizer.Add(wx.StaticText(G2frame.dataWindow,label='Value (0.001-0.999) '),0,WACV) polaVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['PolaVal'],0,nDig=(10,3),typeHint=float,xmin=0.001,xmax=0.999) littleSizer.Add(polaVal,0,WACV) dataSizer.Add(littleSizer,0,) return dataSizer def BackSizer(): global oldFlat def OnBackImage(event): data['background image'][0] = backImage.GetValue() G2frame.ImageZ = GetImageZ(G2frame,data,newRange=True) ResetThresholds() wx.CallAfter(G2plt.PlotExposedImage,G2frame,event=event) def OnDarkImage(event): data['dark image'][0] = darkImage.GetValue() G2frame.ImageZ = GetImageZ(G2frame,data,newRange=True) ResetThresholds() wx.CallAfter(G2plt.PlotExposedImage,G2frame,event=event) def OnFlatBkg(invalid,value,tc): global oldFlat G2frame.ImageZ += int(oldFlat-data['Flat Bkg']) oldFlat = data['Flat Bkg'] ResetThresholds() wx.CallAfter(G2plt.PlotExposedImage,G2frame,event=tc.event) def OnMult(invalid,value,tc): G2frame.ImageZ = GetImageZ(G2frame,data,newRange=True) wx.CallAfter(G2plt.PlotExposedImage,G2frame,event=tc.event) def OnGainMap(event): data['Gain map'] = gainMap.GetValue() G2frame.ImageZ = GetImageZ(G2frame,data,newRange=True) ResetThresholds() wx.CallAfter(G2plt.PlotExposedImage,G2frame,event=event) backSizer = wx.FlexGridSizer(0,6,5,5) oldFlat = data.get('Flat Bkg',0.) backSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Dark image'),0,WACV) Choices = ['',]+G2gd.GetGPXtreeDataNames(G2frame,['IMG ',]) Source = G2frame.GPXtree.GetItemText(G2frame.Image) Choices.pop(Choices.index(Source)) darkImage = wx.ComboBox(parent=G2frame.dataWindow,value=data['dark image'][0],choices=Choices, style=wx.CB_READONLY|wx.CB_DROPDOWN) darkImage.Bind(wx.EVT_COMBOBOX,OnDarkImage) backSizer.Add(darkImage) backSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' multiplier'),0,WACV) darkMult = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['dark image'],1,nDig=(10,3), typeHint=float,OnLeave=OnMult) backSizer.Add(darkMult,0,WACV) backSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Flat Bkg: '),0,WACV) flatbkg = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'Flat Bkg',nDig=(10,0), typeHint=float,OnLeave=OnFlatBkg) backSizer.Add(flatbkg,0,WACV) backSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Background image'),0,WACV) backImage = wx.ComboBox(parent=G2frame.dataWindow,value=data['background image'][0],choices=Choices, style=wx.CB_READONLY|wx.CB_DROPDOWN) backImage.Bind(wx.EVT_COMBOBOX,OnBackImage) backSizer.Add(backImage) backSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' multiplier'),0,WACV) backMult = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['background image'],1,nDig=(10,3), typeHint=float,OnLeave=OnMult) backSizer.Add(backMult,0,WACV) backSizer.Add((5,5),0) backSizer.Add((5,5),0) backSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Gain map'),0,WACV) gainMap = wx.ComboBox(G2frame.dataWindow,value=data['Gain map'],choices=Choices, style=wx.CB_READONLY|wx.CB_DROPDOWN) gainMap.Bind(wx.EVT_COMBOBOX,OnGainMap) backSizer.Add(gainMap) return backSizer def CalibSizer(): def OnNewCalibrant(event): data['calibrant'] = calSel.GetValue().strip() if data['calibrant']: G2frame.dataWindow.ImageEdit.Enable(id=G2G.wxID_IMRECALIBRATE,enable=True) G2frame.dataWindow.ImageEdit.Enable(id=G2G.wxID_IMCALIBRATE,enable=True) G2frame.dataWindow.ImageEdit.Enable(id=G2G.wxID_IMRECALIBALL,enable=True) data['calibskip'] = calFile.Calibrants[data['calibrant']][3] limits = calFile.Calibrants[data['calibrant']][4] data['calibdmin'],data['pixLimit'],data['cutoff'] = limits pixLimit.SetValue(str(limits[1])) cutOff.SetValue(limits[2]) calibSkip.SetValue(str(data['calibskip'])) G2frame.calibDmin.SetValue(limits[0]) else: G2frame.dataWindow.ImageEdit.Enable(id=G2G.wxID_IMRECALIBRATE,enable=False) G2frame.dataWindow.ImageEdit.Enable(id=G2G.wxID_IMCALIBRATE,enable=False) G2frame.dataWindow.ImageEdit.Enable(id=G2G.wxID_IMRECALIBALL,enable=False) def OnCalibSkip(event): data['calibskip'] = int(calibSkip.GetValue()) def OnPixLimit(event): data['pixLimit'] = int(pixLimit.GetValue()) def OnSetRings(event): data['setRings'] = not data['setRings'] G2plt.PlotExposedImage(G2frame,event=event) calibSizer = wx.FlexGridSizer(0,3,5,5) comboSizer = wx.BoxSizer(wx.HORIZONTAL) comboSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Calibrant '),0,WACV) if (GSASIIpath.GetConfigValue('Image_calibrant') and GSASIIpath.GetConfigValue('Image_calibrant') in calList and not data['calibrant']): data['calibrant'] = GSASIIpath.GetConfigValue('Image_calibrant') calSel = wx.ComboBox(parent=G2frame.dataWindow,value=data['calibrant'],choices=calList, style=wx.CB_READONLY|wx.CB_DROPDOWN) calSel.Bind(wx.EVT_COMBOBOX, OnNewCalibrant) comboSizer.Add(calSel,0,WACV) calibSizer.Add(comboSizer,0) comboSizer = wx.BoxSizer(wx.HORIZONTAL) comboSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Calib lines to skip '),0,WACV) calibSkip = wx.ComboBox(parent=G2frame.dataWindow,value=str(data['calibskip']),choices=[str(i) for i in range(25)], style=wx.CB_READONLY|wx.CB_DROPDOWN) calibSkip.Bind(wx.EVT_COMBOBOX, OnCalibSkip) comboSizer.Add(calibSkip,0,WACV) calibSizer.Add(comboSizer,0) comboSizer = wx.BoxSizer(wx.HORIZONTAL) comboSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Min calib d-spacing '),0,WACV) G2frame.calibDmin = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'calibdmin',nDig=(10,2),typeHint=float,xmin=0.25) comboSizer.Add(G2frame.calibDmin,0,WACV) calibSizer.Add(comboSizer,0) comboSizer = wx.BoxSizer(wx.HORIZONTAL) comboSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Min ring I/Ib '),0,WACV) cutOff = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'cutoff',nDig=(10,2),xmin=0.1) comboSizer.Add(cutOff,0,WACV) calibSizer.Add(comboSizer,0) comboSizer = wx.BoxSizer(wx.HORIZONTAL) comboSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Pixel search range '),0,WACV) pixLimit = wx.ComboBox(parent=G2frame.dataWindow,value=str(data['pixLimit']),choices=['1','2','5','10','15','20'], style=wx.CB_READONLY|wx.CB_DROPDOWN) pixLimit.Bind(wx.EVT_COMBOBOX, OnPixLimit) comboSizer.Add(pixLimit,0,WACV) calibSizer.Add(comboSizer,0) comboSizer = wx.BoxSizer(wx.HORIZONTAL) setRings = wx.CheckBox(parent=G2frame.dataWindow,label='Show ring picks?') comboSizer.Add(setRings,0) setRings.Bind(wx.EVT_CHECKBOX, OnSetRings) setRings.SetValue(data['setRings']) calibSizer.Add(comboSizer,0) return calibSizer def GonioSizer(): def OnGlobalEdit(event): Names = [] Items = [] if G2frame.GPXtree.GetCount(): Id, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root) while Id: name = G2frame.GPXtree.GetItemText(Id) if 'IMG' in name: ctrls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Image Controls')) Names.append(name) Items.append(ctrls['GonioAngles']) Id, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie) if len(Names) == 1: G2frame.ErrorDialog('Nothing for global editing','There must be more than one "IMG" pattern') return dlg = G2G.G2HistoDataDialog(G2frame,' Edit sample goniometer data:', 'Edit data',['Omega','Chi','Phi'],['%.2f','%.2f','%.2f'],Names,Items) try: if dlg.ShowModal() == wx.ID_OK: Id, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root) while Id: name = G2frame.GPXtree.GetItemText(Id) if 'IMG' in name: ctrls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Image Controls')) vals = Items[Names.index(name)] ctrls['GonioAngles'] = vals Id, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie) finally: dlg.Destroy() G2frame.GPXtree.SelectItem(G2frame.PickId) gonioSizer = wx.BoxSizer(wx.HORIZONTAL) names = ['Omega','Chi','Phi'] gonioSizer.Add(wx.StaticText(G2frame.dataWindow,-1,'Sample goniometer angles: '),0,WACV) for i,name in enumerate(names): gonioSizer.Add(wx.StaticText(G2frame.dataWindow,-1,name),0,WACV) angle = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['GonioAngles'],i,nDig=(8,2),typeHint=float) gonioSizer.Add(angle,0,WACV) globEdit = wx.Button(G2frame.dataWindow,-1,'Global edit') globEdit.Bind(wx.EVT_BUTTON,OnGlobalEdit) gonioSizer.Add(globEdit,0,WACV) return gonioSizer # UpdateImageControls: Image Controls main code #fix for old files: if 'azmthOff' not in data: data['azmthOff'] = 0.0 if 'background image' not in data: data['background image'] = ['',-1.0] if 'dark image' not in data: data['dark image'] = ['',-1.0] if 'centerAzm' not in data: data['centerAzm'] = False if 'Oblique' not in data: data['Oblique'] = [0.5,False] if 'PolaVal' not in data: data['PolaVal'] = [0.99,False] if 'IfPink' not in data: data['IfPink'] = False #end fix if IntegrateOnly: Masks = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.Image,'Masks')) # Mhash = hash(str(Masks)) # TODO: implement this to save integration time (?) # if Mhash != oldMhash: # t0 = time.time() useMask = G2img.MakeUseMask(data,Masks,blkSize) # print(' Use new mask; make mask time: %.3f'%(time.time()-t0)) # oldMhash = Mhash OnIntegrate(None,useTA=useTA,useMask=useMask) return G2frame.GetStatusBar().SetStatusText('* Global parameters in Multi-dist recalib.',1) colorList = sorted([m for m in mpl.cm.datad.keys() ],key=lambda s: s.lower()) #if not m.endswith("_r") calList = sorted([m for m in calFile.Calibrants.keys()],key=lambda s: s.lower()) typeList = ['PWDR - powder diffraction data','SASD - small angle scattering data',] if not data.get('type'): #patch for old project files data['type'] = 'PWDR' typeDict = {'PWDR':typeList[0],'SASD':typeList[1],} G2frame.dataWindow.ClearData() G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.ImageMenu) G2frame.Bind(wx.EVT_MENU, OnCalibrate, id=G2G.wxID_IMCALIBRATE) G2frame.Bind(wx.EVT_MENU, OnRecalibrate, id=G2G.wxID_IMRECALIBRATE) G2frame.Bind(wx.EVT_MENU, OnRecalibAll, id=G2G.wxID_IMRECALIBALL) G2frame.Bind(wx.EVT_MENU, OnDistRecalib, id=G2G.wxID_IMDISTRECALIB) G2frame.Bind(wx.EVT_MENU, OnClearCalib, id=G2G.wxID_IMCLEARCALIB) # if data.get('calibrant'): # mode = True # else: # mode = False # G2frame.Enable(id=G2G.wxID_IMRECALIBRATE,enable=mode) # G2frame.Enable(id=G2G.wxID_IMCALIBRATE,enable=mode) # G2frame.Enable(id=G2G.wxID_IMRECALIBALL,enable=mode) G2frame.Bind(wx.EVT_MENU, OnIntegrate, id=G2G.wxID_IMINTEGRATE) G2frame.Bind(wx.EVT_MENU, OnIntegrateAll, id=G2G.wxID_INTEGRATEALL) G2frame.Bind(wx.EVT_MENU, OnCopyControls, id=G2G.wxID_IMCOPYCONTROLS) G2frame.Bind(wx.EVT_MENU, OnCopySelected, id=G2G.wxID_IMCOPYSELECTED) G2frame.Bind(wx.EVT_MENU, OnSaveControls, id=G2G.wxID_IMSAVECONTROLS) G2frame.Bind(wx.EVT_MENU, OnSaveMultiControls, id=G2G.wxID_SAVESELECTEDCONTROLS) G2frame.Bind(wx.EVT_MENU, OnLoadControls, id=G2G.wxID_IMLOADCONTROLS) G2frame.Bind(wx.EVT_MENU, OnLoadMultiControls, id=G2G.wxID_LOADELECTEDCONTROLS) G2frame.Bind(wx.EVT_MENU, OnTransferAngles, id=G2G.wxID_IMXFERCONTROLS) G2frame.Bind(wx.EVT_MENU, OnResetDist, id=G2G.wxID_IMRESETDIST) def OnDestroy(event): G2frame.autoIntFrame = None def OnAutoInt(event): if G2frame.autoIntFrame: # ensure only one open at a time G2frame.autoIntFrame.Raise() return PollTime = GSASIIpath.GetConfigValue('Autoint_PollTime',30.) G2frame.autoIntFrame = AutoIntFrame(G2frame,PollTime=PollTime) # debug code to reload code for window on each use #import GSASIIimgGUI #reload(GSASIIimgGUI) #G2frame.autoIntFrame = GSASIIimgGUI.AutoIntFrame(G2frame,PollTime=PollTime) G2frame.autoIntFrame.Bind(wx.EVT_WINDOW_DESTROY,OnDestroy) # clean up name on window close G2frame.Bind(wx.EVT_MENU, OnAutoInt, id=G2G.wxID_IMAUTOINTEG) def OnIntPDFtool(event): import subprocess ex = sys.executable if sys.platform == "darwin": # mac requires pythonw which is not always reported as sys.executable if os.path.exists(ex+'w'): ex += 'w' if G2frame.GSASprojectfile: project = os.path.abspath(G2frame.GSASprojectfile) else: project = '' subprocess.Popen([ex,os.path.join(GSASIIpath.path2GSAS2,'GSASIIIntPDFtool.py'),project]) G2frame.Bind(wx.EVT_MENU, OnIntPDFtool, id=G2G.wxID_IMINTEGPDFTOOL) mainSizer = G2frame.dataWindow.GetSizer() mainSizer.Add((5,10),0) mainSizer.Add(ComboSizer(),0,wx.ALIGN_LEFT) mainSizer.Add((5,5),0) Range = data['range'] # allows code to be same in Masks MaxSizer = MaxSizer() #keep this so it can be changed in BackSizer mainSizer.Add(MaxSizer,0,wx.ALIGN_LEFT|wx.EXPAND|wx.ALL) mainSizer.Add((5,5),0) DataSizer = wx.FlexGridSizer(0,2,5,0) DataSizer.Add(CalibCoeffSizer(),0) DataSizer.Add(IntegrateSizer(),0) mainSizer.Add(DataSizer,0) mainSizer.Add((5,5),0) mainSizer.Add(BackSizer(),0) mainSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Calibration controls:'),0) mainSizer.Add((5,5),0) mainSizer.Add(CalibSizer(),0) mainSizer.Add((5,5),0) mainSizer.Add(GonioSizer(),0) G2frame.dataWindow.SetDataSize()
################################################################################ ##### Masks ################################################################################
[docs]def CleanupMasks(data): '''If a mask creation is not completed, an empty mask entry is created in the masks array. This cleans them out. It is called when the masks page is first loaded and before saving them or after reading them in. This should also probably be done before they are used for integration. ''' for key in ['Points','Rings','Arcs','Polygons',]: data[key] = data.get(key,[]) l1 = len(data[key]) data[key] = [i for i in data[key] if len(i)] l2 = len(data[key]) if GSASIIpath.GetConfigValue('debug') and l1 != l2: print ('DBG_Mask Cleanup: %s was %d entries, now %d'%(key,l1,l2))
[docs]def UpdateMasks(G2frame,data): '''Shows and handles the controls on the "Masks" data tree entry ''' def OnTextMsg(event): Obj = event.GetEventObject() Obj.SetToolTipString('Drag this mask on 2D Powder Image with mouse to change ') def Replot(*args,**kwargs): wx.CallAfter(G2plt.PlotExposedImage,G2frame) def newReplot(*args,**kwargs): wx.CallAfter(G2plt.PlotExposedImage,G2frame,newPlot=True) def onDeleteMask(event): Obj = event.GetEventObject() typ = Obj.locationcode.split('+')[1] num = int(Obj.locationcode.split('+')[2]) del(data[typ][num]) wx.CallAfter(UpdateMasks,G2frame,data) G2plt.PlotExposedImage(G2frame,event=event) def OnSpotChange(event): r,c = event.GetRow(),event.GetCol() if c == 2: del Spots[r] SpotTable.DeleteRow(r) else: Spots[r][2] = float(SpotGrid.GetCellValue(r,c)) SpotGrid.ForceRefresh() wx.CallAfter(UpdateMasks,G2frame,data) G2plt.PlotExposedImage(G2frame,event=event) event.Skip() def onDeleteFrame(event): data['Frames'] = [] wx.CallAfter(UpdateMasks,G2frame,data) G2plt.PlotExposedImage(G2frame,event=event) def OnCopyMask(event): Names = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',]) if len(Names) == 1: G2frame.ErrorDialog('Nothing to copy masks to','There must be more than one "IMG" pattern') return Source = G2frame.GPXtree.GetItemText(G2frame.Image) Names.pop(Names.index(Source)) Data = copy.deepcopy(data) Thresh = Data.pop('Thresholds') # & remove it as well dlg = G2G.G2MultiChoiceDialog(G2frame,'Copy mask data','Copy masks from '+Source+' to:',Names) try: if dlg.ShowModal() == wx.ID_OK: items = dlg.GetSelections() for item in items: name = Names[item] Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,name) MId = G2gd.GetGPXtreeItemId(G2frame,Id,'Masks') Mask = G2frame.GPXtree.GetItemPyData(MId) Mask.update(copy.deepcopy(Data)) Mask['Thresholds'][1][0] = Thresh[1][0] #copy only lower threshold G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Masks'),Mask) finally: dlg.Destroy() def OnSaveMask(event): CleanupMasks(data) pth = G2G.GetExportPath(G2frame) dlg = wx.FileDialog(G2frame, 'Choose image mask file', pth, '', 'image mask files (*.immask)|*.immask',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT) try: if dlg.ShowModal() == wx.ID_OK: filename = dlg.GetPath() filename = os.path.splitext(filename)[0]+'.immask' File = open(filename,'w') keys = ['Points','Rings','Arcs','Polygons','Xlines','Ylines','Frames','Thresholds'] for key in keys: File.write(key+':'+str(data[key])+'\n') File.close() finally: dlg.Destroy() def OnLoadMask(event): if event.Id == G2G.wxID_MASKLOADNOT: ignoreThreshold = True else: ignoreThreshold = False pth = G2G.GetImportPath(G2frame) if not pth: pth = '.' dlg = wx.FileDialog(G2frame, 'Choose image mask file', pth, '', 'image mask files (*.immask)|*.immask',wx.FD_OPEN) try: if dlg.ShowModal() == wx.ID_OK: filename = dlg.GetPath() G2fil.readMasks(filename,data,ignoreThreshold) wx.CallAfter(UpdateMasks,G2frame,data) G2plt.PlotExposedImage(G2frame,event=event) finally: dlg.Destroy() def OnFindSpotMask(event): 'Do auto search for spot masks' try: if wx.MessageDialog(G2frame.dataWindow,'NB: This is slow (5-10min)', 'Spot mask search', wx.OK|wx.CANCEL).ShowModal() == wx.ID_OK: Controls = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.Image,'Image Controls')) wave = Controls['wavelength'] LUtth = np.array(Controls['IOtth']) dsp0 = wave/(2.0*sind(LUtth[0]/2.0)) dsp1 = wave/(2.0*sind(LUtth[1]/2.0)) x0 = G2img.GetDetectorXY2(dsp0,0.0,Controls)[0] x1 = G2img.GetDetectorXY2(dsp1,0.0,Controls)[0] if not np.any(x0) or not np.any(x1): raise Exception nChans = int(1000*(x1-x0)/Controls['pixelSize'][0])//2 dlg = wx.ProgressDialog("Auto spot masking for %d bins"%nChans,"Processed 2-theta rings = ",nChans+3, style = wx.PD_ELAPSED_TIME|wx.PD_CAN_ABORT) time0 = time.time() data['SpotMask']['spotMask'] = G2img.AutoSpotMask(G2frame.ImageZ,data,Controls,nChans,dlg) print(' Spot masksearch time: %.2f m'%((time.time()-time0)/60.)) wx.CallAfter(UpdateMasks,G2frame,data) wx.CallAfter(G2plt.PlotExposedImage,G2frame,event=event) else: print(' Spot mask search not done') except: print('Invalid limits - spot mask search not done') def OnAutoFindSpotMask(event): Names = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',]) dlg = G2G.G2MultiChoiceDialog(G2frame,'Automatic spot mask search','Select images to spot mask:',Names) try: if dlg.ShowModal() == wx.ID_OK: items = dlg.GetSelections() G2frame.EnablePlot = False for item in items: name = Names[item] print ('Spot search for'+name) G2frame.Image = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,name) Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.Image,'Image Controls')) Mask = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.Image,'Masks')) G2frame.ImageZ = GetImageZ(G2frame,Controls) wave = Controls['wavelength'] LUtth = np.array(Controls['IOtth']) dsp0 = wave/(2.0*sind(LUtth[0]/2.0)) dsp1 = wave/(2.0*sind(LUtth[1]/2.0)) x0 = G2img.GetDetectorXY2(dsp0,0.0,Controls)[0] x1 = G2img.GetDetectorXY2(dsp1,0.0,Controls)[0] if not np.any(x0) or not np.any(x1): raise Exception nChans = int(1000*(x1-x0)/Controls['pixelSize'][0])//2 dlg = wx.ProgressDialog("Spot mask search for %d bins"%nChans,"Processed 2-theta rings = ",nChans+3, style = wx.PD_ELAPSED_TIME|wx.PD_CAN_ABORT) time0 = time.time() Mask['SpotMask']['spotMask'] = G2img.AutoSpotMask(G2frame.ImageZ,Mask,Controls,nChans,dlg) print(' Spot mask search time: %.2f m'%((time.time()-time0)/60.)) except: print('Invalid limits - spot mask search not done') finally: dlg.Destroy() G2plt.PlotExposedImage(G2frame,event=None) def OnDeleteSpotMask(event): data['Points'] = [] wx.CallAfter(UpdateMasks,G2frame,data) G2plt.PlotExposedImage(G2frame,newPlot=True,event=event) def ToggleSpotMaskMode(event): G2plt.ToggleMultiSpotMask(G2frame) def OnNewArcMask(event): 'Start a new arc mask' G2frame.MaskKey = 'a' G2plt.OnStartMask(G2frame) def OnNewRingMask(event): 'Start a new ring mask' G2frame.MaskKey = 'r' G2plt.OnStartMask(G2frame) def OnNewXlineMask(event): 'Start a new x-line mask' print('x') G2frame.MaskKey = 'x' G2plt.OnStartMask(G2frame) def OnNewYlineMask(event): 'Start a new y-line mask' G2frame.MaskKey = 'y' G2plt.OnStartMask(G2frame) def OnNewPolyMask(event): 'Start a new polygon mask' G2frame.MaskKey = 'p' G2plt.OnStartMask(G2frame) def OnNewFrameMask(event): 'Start a new Frame mask' G2frame.MaskKey = 'f' G2plt.OnStartMask(G2frame) def MaxSizer(): '''Defines a sizer with sliders and TextCtrl widgets for controlling the colormap for the image, as well as callback routines. ''' def OnNewVal(invalid,value,tc): '''Called when a Imax or Imin value is typed into a Validated TextCrtl (which puts the value into the data['range'] nested list). This adjusts the slider positions to match the current values ''' scaleSel.SetSelection(len(scaleChoices)-1) r11 = min(max(Range[1][1],Range[1][0]+1),Range[0][1]) # keep values in range if r11 != Range[1][1]: Range[1][1] = r11 maxVal.SetValue(int(Range[1][1])) r10 = max(min(Range[1][0],Range[1][1]-1),Range[0][0]) if r10 != Range[1][0]: Range[1][0] = r10 minVal.SetValue(int(Range[1][0])) sqrtDeltZero = math.sqrt(max(1.0,Range[0][1]-max(0.0,Range[1][0])-1)) # sqrt(Imax0-Imin-1) sqrtDeltOne = math.sqrt(max(1.0,Range[1][1]-max(0.0,Range[1][0])-1)) # sqrt(Imax-Imin-1) sv1 = min(100,max(0,int(0.5+100.*sqrtDeltOne/sqrtDeltZero))) maxSel.SetValue(sv1) DeltOne = max(1.0,Range[1][1]-max(0.0,Range[0][0])-1) sv0 = min(100,max(0,int(0.5+100.*(Range[1][0]-Range[0][0])/DeltOne))) minSel.SetValue(sv0) new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('2D Powder Image','mpl',newImage=False) Page.ImgObj.set_clim([Range[1][0],Range[1][1]]) if mplOld: Page.canvas.draw() else: Page.canvas.draw_idle() G2frame.prevMaxValue = None def OnMaxSlider(event): val = maxSel.GetValue() if G2frame.prevMaxValue == val: return # if this val has been processed, no need to repeat scaleSel.SetSelection(len(scaleChoices)-1) G2frame.prevMaxValue = val sqrtDeltZero = math.sqrt(max(1.0,Range[0][1]-max(0.0,Range[1][0])-1)) # sqrt(Imax0-Imin-1) Range[1][1] = int(0.5 + (val * sqrtDeltZero / 100.)**2 + Range[1][0] + 1) maxVal.SetValue(int(0.5+Range[1][1])) DeltOne = max(1.0,Range[1][1]-max(0.0,Range[0][0])-1) minSel.SetValue(int(0.5 + 100*(Range[1][0]/DeltOne))) sv0 = min(100,max(0,int(0.5+100.*(Range[1][0]-Range[0][0])/DeltOne))) minSel.SetValue(sv0) new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('2D Powder Image','mpl',newImage=False) Page.ImgObj.set_clim([Range[1][0],Range[1][1]]) if mplOld: Page.canvas.draw() else: Page.canvas.draw_idle() G2frame.prevMinValue = None def OnMinSlider(event): val = minSel.GetValue() scaleSel.SetSelection(len(scaleChoices)-1) if G2frame.prevMinValue == val: return # if this val has been processed, no need to repeat G2frame.prevMinValue = val DeltOne = max(1.0,Range[1][1]-max(0.0,Range[0][0])-1) # Imax-Imin0-1 Range[1][0] = max(0,int(0.5 + val * DeltOne / 100 + Range[0][0])) minVal.SetValue(int(Range[1][0])) sqrtDeltZero = math.sqrt(max(1.0,Range[0][1]-max(0.0,Range[1][0])-1)) # sqrt(Imax0-Imin-1) sqrtDeltOne = math.sqrt(max(1.0,Range[1][1]-max(0.0,Range[1][0])-1)) # sqrt(Imax-Imin-1) sv1 = min(100,max(0,int(0.5+100.*sqrtDeltOne/sqrtDeltZero))) maxSel.SetValue(sv1) new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('2D Powder Image','mpl',newImage=False) Page.ImgObj.set_clim([Range[1][0],Range[1][1]]) if mplOld: Page.canvas.draw() else: Page.canvas.draw_idle() def OnAutoSet(event): '''Responds to a button labeled 95%, etc; Sets the Imax and Imin values for the image so that 95% (etc.) of pixels are inside the color map limits. An equal number of pixels are dropped at the minimum and maximum levels. ''' try: val = int(event.GetEventObject().GetStringSelection()[:-1]) margin = (100-val)/2. except: margin = 0 event.GetEventObject().SetSelection(0) new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('2D Powder Image','mpl',newImage=False) if margin == 0: Range[1] = list(Range[0]) else: Range[1][0] = int(np.percentile(Page.ImgObj.get_array().compressed(),margin)) Range[1][1] = int(np.percentile(Page.ImgObj.get_array().compressed(),100-margin)) sqrtDeltZero = math.sqrt(max(1.0,Range[0][1]-max(0.0,Range[1][0])-1)) # sqrt(Imax0-Imin-1) sqrtDeltOne = math.sqrt(max(1.0,Range[1][1]-max(0.0,Range[1][0])-1)) # sqrt(Imax-Imin-1) sv1 = min(100,max(0,int(0.5+100.*sqrtDeltOne/sqrtDeltZero))) maxSel.SetValue(sv1) DeltOne = max(1.0,Range[1][1]-max(0.0,Range[0][0])-1) sv0 = min(100,max(0,int(0.5+100.*(Range[1][0]-Range[0][0])/DeltOne))) minSel.SetValue(sv0) minVal.SetValue(int(Range[1][0])) maxVal.SetValue(int(Range[1][1])) new,plotNum,Page,Plot,lim = G2frame.G2plotNB.FindPlotTab('2D Powder Image','mpl',newImage=False) Page.ImgObj.set_clim([Range[1][0],Range[1][1]]) if mplOld: Page.canvas.draw() else: Page.canvas.draw_idle() mplv = mpl.__version__.split('.') mplOld = mplv[0] == '1' and int(mplv[1]) < 4 # use draw_idle for newer matplotlib versions # Plot color scaling uses limits as below: # (Imin0, Imax0) => Range[0] = data['range'][0] # lowest to highest pixel intensity # [Imin, Imax] => Range[1] = data['range'][1] # lowest to highest pixel intensity on cmap scale maxSizer = wx.BoxSizer(wx.VERTICAL) slideSizer = wx.FlexGridSizer(2,3,5,5) slideSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Max intensity'),0,WACV) # maxSel is a slider with 101 steps scaled from Imin+1 to Imax0 with sqrt scaling # slider value = sv = 100 * sqrt((Imax-Imin-1)/(Imax0-Imin-1)) # Imax = (sv * sqrt(Imax0-Imin-1) / 100)**2 + Imin + 1 sqrtDeltZero = math.sqrt(max(1.0,Range[0][1]-max(0.0,Range[1][0])-1)) # sqrt(Imax0-Imin-1) sqrtDeltOne = math.sqrt(max(1.0,Range[1][1]-max(0.0,Range[1][0])-1)) # sqrt(Imax-Imin-1) sv1 = min(100,max(0,int(0.5+100.*sqrtDeltOne/sqrtDeltZero))) maxSel = wx.Slider(parent=G2frame.dataWindow,style=wx.SL_HORIZONTAL,value=sv1) maxVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,Range[1],1,xmin=Range[0][0]+1, xmax=Range[0][1],OnLeave=OnNewVal) slideSizer.Add(maxVal,0,WACV) slideSizer.Add(maxSel,flag=wx.EXPAND|wx.ALL) slideSizer.AddGrowableCol(2) maxSel.Bind(wx.EVT_SLIDER, OnMaxSlider) slideSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Min intensity'),0,WACV) # minSel is a slider with 101 steps scaled from Imin0 to Imax-1 with linear scaling # slider value = sv0 = 100 * (Imin-Imin0)/(Imax-Imin0-1) # Imin = sv0 * (Imax-Imin0-1) / 100 + Imin0 DeltOne = max(1.0,Range[1][1]-max(0.0,Range[0][0])-1) # Imax-Imin0-1 sv0 = min(100,max(0,int(0.5+100.*(Range[1][0]-Range[0][0])/DeltOne))) minVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,Range[1],0, xmax=Range[0][1],typeHint=int,OnLeave=OnNewVal) slideSizer.Add(minVal,0,WACV) minSel = wx.Slider(parent=G2frame.dataWindow,style=wx.SL_HORIZONTAL,value=sv0) slideSizer.Add(minSel,flag=wx.EXPAND|wx.ALL) minSel.Bind(wx.EVT_SLIDER, OnMinSlider) maxSizer.Add(slideSizer,flag=wx.EXPAND|wx.ALL) autoSizer = wx.BoxSizer(wx.HORIZONTAL) autoSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Auto scaler '),0,WACV) scaleChoices = ("100%","99%","95%","90%","80%","?") scaleSel = wx.Choice(G2frame.dataWindow,choices=scaleChoices,size=(-1,-1)) if (Range[1][0] == Range[0][0] and Range[1][1] == Range[0][1]): scaleSel.SetSelection(0) else: scaleSel.SetSelection(len(scaleChoices)-1) scaleSel.Bind(wx.EVT_CHOICE,OnAutoSet) autoSizer.Add(scaleSel,0,WACV) maxSizer.Add(autoSizer) return maxSizer def OnDelBtn(event): data['SpotMask'] = {'esdMul':3.,'spotMask':None} wx.CallAfter(UpdateMasks,G2frame,data) G2frame.dataWindow.ClearData() startScroll = None if G2frame.dataWindow: startScroll = G2frame.dataWindow.GetScrollPos(wx.VERTICAL) # save scroll position else: CleanupMasks(data) # posting page for 1st time; clean out anything unfinished G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.MaskMenu) G2frame.Bind(wx.EVT_MENU, OnCopyMask, id=G2G.wxID_MASKCOPY) G2frame.Bind(wx.EVT_MENU, OnLoadMask, id=G2G.wxID_MASKLOAD) G2frame.Bind(wx.EVT_MENU, OnLoadMask, id=G2G.wxID_MASKLOADNOT) G2frame.Bind(wx.EVT_MENU, OnSaveMask, id=G2G.wxID_MASKSAVE) G2frame.Bind(wx.EVT_MENU, OnFindSpotMask, id=G2G.wxID_FINDSPOTS) G2frame.Bind(wx.EVT_MENU, OnAutoFindSpotMask, id=G2G.wxID_AUTOFINDSPOTS) G2frame.Bind(wx.EVT_MENU, OnDeleteSpotMask, id=G2G.wxID_DELETESPOTS) G2frame.Bind(wx.EVT_MENU, ToggleSpotMaskMode, id=G2G.wxID_NEWMASKSPOT) G2frame.Bind(wx.EVT_MENU, OnNewArcMask, id=G2G.wxID_NEWMASKARC) G2frame.Bind(wx.EVT_MENU, OnNewRingMask, id=G2G.wxID_NEWMASKRING) G2frame.Bind(wx.EVT_MENU, OnNewXlineMask, id=G2G.wxID_NEWMASKXLINE) G2frame.Bind(wx.EVT_MENU, OnNewYlineMask, id=G2G.wxID_NEWMASKYLINE) G2frame.Bind(wx.EVT_MENU, OnNewPolyMask, id=G2G.wxID_NEWMASKPOLY) G2frame.Bind(wx.EVT_MENU, OnNewFrameMask, id=G2G.wxID_NEWMASKFRAME) if G2frame.MaskKey == 'f': G2frame.GetStatusBar().SetStatusText('Frame mask active - LB pick next point, RB close polygon',1) elif G2frame.MaskKey == 'p': G2frame.GetStatusBar().SetStatusText('Polygon mask active - LB pick next point, RB close polygon',1) elif G2frame.MaskKey == 'a': G2frame.GetStatusBar().SetStatusText('Arc mask active - LB pick arc location',1) elif G2frame.MaskKey == 'r': G2frame.GetStatusBar().SetStatusText('Ring mask active - LB pick ring location',1) elif G2frame.MaskKey == 'x': G2frame.GetStatusBar().SetStatusText('X-line mask active - LB pick x line of pixels',1) elif G2frame.MaskKey == 'y': G2frame.GetStatusBar().SetStatusText('Y-line mask active - LB pick y line of pixels',1) else: G2frame.GetStatusBar().SetStatusText("To add mask: press a,r,s,x,y,p or f on 2D image for arc/ring/spot/xline/yline/polygon/frame",1) mainSizer = G2frame.dataWindow.GetSizer() mainSizer.Add((5,10),0) thresh = data['Thresholds'] #min/max intensity range Spots = data['Points'] #x,y,radius in mm Rings = data['Rings'] #radius, thickness Polygons = data['Polygons'] #3+ x,y pairs if 'Xlines' not in data: #single rows/columns of bad pixels data['Xlines'] = [] data['Ylines'] = [] Xlines = data['Xlines'] Ylines = data['Ylines'] # not a good place for patch -- this not always called if 'Frames' not in data: data['Frames'] = [] if 'SpotMask' not in data: data['SpotMask'] = {'esdMul':3.,'spotMask':None} frame = data['Frames'] #3+ x,y pairs Arcs = data['Arcs'] #radius, start/end azimuth, thickness ###################################################################### CId = G2gd.GetGPXtreeItemId(G2frame,G2frame.Image,'Image Controls') controlData = G2frame.GPXtree.GetItemPyData(CId) Range = controlData['range'] MaxSizer = MaxSizer() #keep this so it can be changed in BackSizer mainSizer.Add(MaxSizer,0,wx.ALIGN_LEFT|wx.EXPAND|wx.ALL) littleSizer = wx.FlexGridSizer(0,3,0,5) littleSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Lower/Upper limits '),0,WACV) Text = wx.TextCtrl(G2frame.dataWindow,value=str(thresh[0][0]),style=wx.TE_READONLY) littleSizer.Add(Text,0,WACV) Text.SetBackgroundColour(VERY_LIGHT_GREY) Text = wx.TextCtrl(G2frame.dataWindow,value=str(thresh[0][1]),style=wx.TE_READONLY) littleSizer.Add(Text,0,WACV) Text.SetBackgroundColour(VERY_LIGHT_GREY) littleSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Lower/Upper thresholds '),0,WACV) lowerThreshold = G2G.ValidatedTxtCtrl(G2frame.dataWindow,loc=thresh[1],key=0, xmin=thresh[0][0],OnLeave=newReplot,typeHint=int) littleSizer.Add(lowerThreshold,0,WACV) upperThreshold = G2G.ValidatedTxtCtrl(G2frame.dataWindow,loc=thresh[1],key=1, xmax=thresh[0][1],OnLeave=newReplot,typeHint=int) littleSizer.Add(upperThreshold,0,WACV) mainSizer.Add(littleSizer,0,) spotSizer = wx.BoxSizer(wx.HORIZONTAL) data['SpotMask']['esdMul'] = float(data['SpotMask']['esdMul']) spotSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Select n*sigma spot rejection (n=1-10): '),0,WACV) spotSizer.Add(G2G.ValidatedTxtCtrl(G2frame.dataWindow,loc=data['SpotMask'], key='esdMul',xmin=1.,xmax=10.,size=(40,25)),0,WACV) numPix = 0 if data['SpotMask']['spotMask'] is not None: numPix = np.count_nonzero(data['SpotMask']['spotMask']) spotSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Number of pixels in spot mask: %d '%numPix),0,WACV) delbtn = wx.Button(G2frame.dataWindow,label='Clear spot mask') delbtn.Bind(wx.EVT_BUTTON,OnDelBtn) spotSizer.Add(delbtn,0,WACV) mainSizer.Add(spotSizer,0) if len(Spots): lbl = wx.StaticText(parent=G2frame.dataWindow,label=' Spot masks(on plot LB drag to move, shift-LB drag to resize, RB to delete)') lbl.SetBackgroundColour(wx.Colour(200,200,210)) mainSizer.Add(lbl,0,wx.EXPAND,0) colTypes = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_FLOAT+':10,2',wg.GRID_VALUE_BOOL] colIds = ['position, mm','diameter, mm','Delete?'] rowIds = [str(i) for i in range(len(Spots))] table = [['%.2f,%.2f'%(item[0],item[1]),item[2],False] for item in Spots] SpotTable = G2G.Table(table,rowLabels=rowIds,colLabels=colIds,types=colTypes) SpotGrid = G2G.GSGrid(G2frame.dataWindow) SpotGrid.SetTable(SpotTable,True) SpotGrid.AutoSizeColumns(True) SpotGrid.SetColSize(1,80) for r in range(len(Spots)): SpotGrid.SetCellStyle(r,0,VERY_LIGHT_GREY,True) if 'phoenix' in wx.version(): SpotGrid.Bind(wg.EVT_GRID_CELL_CHANGED, OnSpotChange) else: SpotGrid.Bind(wg.EVT_GRID_CELL_CHANGE, OnSpotChange) mainSizer.Add(SpotGrid,0,) if Rings: lbl = wx.StaticText(parent=G2frame.dataWindow,label=' Ring masks') lbl.SetBackgroundColour(wx.Colour(200,200,210)) mainSizer.Add(lbl,0,wx.EXPAND,0) littleSizer = wx.FlexGridSizer(0,3,0,5) littleSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' 2-theta,deg'),0,WACV) littleSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' thickness, deg'),0,WACV) littleSizer.Add((5,0),0) for i in range(len(Rings)): if Rings[i]: ringText = wx.TextCtrl(parent=G2frame.dataWindow,value=("%.3f" % (Rings[i][0])), style=wx.TE_READONLY) ringText.SetBackgroundColour(VERY_LIGHT_GREY) ringText.Bind(wx.EVT_ENTER_WINDOW,OnTextMsg) littleSizer.Add(ringText,0,WACV) ringThick = G2G.ValidatedTxtCtrl(G2frame.dataWindow,loc=Rings[i],key=1, xmin=0.001,xmax=1.,OnLeave=Replot,nDig=[8,3]) littleSizer.Add(ringThick,0,WACV) ringDelete = G2G.G2LoggedButton(G2frame.dataWindow,label='delete?', locationcode='Delete+Rings+'+str(i),handler=onDeleteMask) littleSizer.Add(ringDelete,0,WACV) mainSizer.Add(littleSizer,0,) if Arcs: lbl = wx.StaticText(parent=G2frame.dataWindow,label=' Arc masks') lbl.SetBackgroundColour(wx.Colour(200,200,210)) mainSizer.Add(lbl,0,wx.EXPAND,0) littleSizer = wx.FlexGridSizer(0,4,0,5) littleSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' 2-theta,deg'),0,WACV) littleSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' azimuth, deg'),0,WACV) littleSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' thickness, deg'),0,WACV) littleSizer.Add((5,0),0) for i in range(len(Arcs)): if Arcs[i]: tth,azimuth,thick = Arcs[i] arcText = wx.TextCtrl(parent=G2frame.dataWindow,value=("%.3f" % (tth)), style=wx.TE_READONLY) arcText.SetBackgroundColour(VERY_LIGHT_GREY) arcText.Bind(wx.EVT_ENTER_WINDOW,OnTextMsg) littleSizer.Add(arcText,0,WACV) azmText = wx.TextCtrl(parent=G2frame.dataWindow,value=("%d,%d" % (azimuth[0],azimuth[1])), style=wx.TE_READONLY) azmText.SetBackgroundColour(VERY_LIGHT_GREY) azmText.Bind(wx.EVT_ENTER_WINDOW,OnTextMsg) littleSizer.Add(azmText,0,WACV) arcThick = G2G.ValidatedTxtCtrl(G2frame.dataWindow,loc=Arcs[i],key=2, xmin=0.001,xmax=20.,OnLeave=Replot,nDig=[8,3]) littleSizer.Add(arcThick,0,WACV) arcDelete = G2G.G2LoggedButton(G2frame.dataWindow,label='delete?', locationcode='Delete+Arcs+'+str(i),handler=onDeleteMask) littleSizer.Add(arcDelete,0,WACV) mainSizer.Add(littleSizer,0,) if Xlines: lbl = wx.StaticText(parent=G2frame.dataWindow,label=' X line masks') lbl.SetBackgroundColour(wx.Colour(200,200,210)) mainSizer.Add(lbl,0,wx.EXPAND,0) littleSizer = wx.FlexGridSizer(0,2,0,5) for i in range(len(Xlines)): if Xlines[i]: littleSizer.Add(wx.StaticText(G2frame.dataWindow,label='at Y-pixel: %d'%(Xlines[i])),0,WACV) xlineDelete = G2G.G2LoggedButton(G2frame.dataWindow,label='delete?', locationcode='Delete+Xlines+'+str(i),handler=onDeleteMask) littleSizer.Add(xlineDelete,0,WACV) mainSizer.Add(littleSizer,0,) if Ylines: lbl = wx.StaticText(parent=G2frame.dataWindow,label=' Y line masks') lbl.SetBackgroundColour(wx.Colour(200,200,210)) mainSizer.Add(lbl,0,wx.EXPAND,0) littleSizer = wx.FlexGridSizer(0,2,0,5) for i in range(len(Ylines)): if Ylines[i]: littleSizer.Add(wx.StaticText(G2frame.dataWindow,label='at X-pixel: %d'%(Ylines[i])),0,WACV) ylineDelete = G2G.G2LoggedButton(G2frame.dataWindow,label='delete?', locationcode='Delete+Ylines+'+str(i),handler=onDeleteMask) littleSizer.Add(ylineDelete,0,WACV) mainSizer.Add(littleSizer,0,) if Polygons: lbl = wx.StaticText(parent=G2frame.dataWindow, label=' Polygon masks (on plot LB vertex drag to move, RB vertex drag to insert)') lbl.SetBackgroundColour(wx.Colour(200,200,210)) mainSizer.Add(lbl,0,wx.EXPAND,0) littleSizer = wx.FlexGridSizer(0,2,0,5) for i in range(len(Polygons)): if Polygons[i]: polyList = [] for x,y in Polygons[i]: polyList.append("%.2f, %.2f"%(x,y)) polyText = wx.ComboBox(G2frame.dataWindow,value=polyList[0],choices=polyList,style=wx.CB_READONLY) littleSizer.Add(polyText,0,WACV) polyDelete = G2G.G2LoggedButton(G2frame.dataWindow,label='delete?', locationcode='Delete+Polygons+'+str(i),handler=onDeleteMask) littleSizer.Add(polyDelete,0,WACV) mainSizer.Add(littleSizer,0,) if frame: lbl = wx.StaticText(parent=G2frame.dataWindow, label=' Frame mask (on plot LB vertex drag to move, RB vertex drag to insert)') lbl.SetBackgroundColour(wx.Colour(200,200,210)) mainSizer.Add(lbl,0,wx.EXPAND,0) littleSizer = wx.FlexGridSizer(0,2,0,5) frameList = [] for x,y in frame: frameList.append("%.2f, %.2f"%(x,y)) frameText = wx.ComboBox(G2frame.dataWindow,value=frameList[0],choices=frameList,style=wx.CB_READONLY) littleSizer.Add(frameText,0,WACV) frameDelete = G2G.G2LoggedButton(G2frame.dataWindow,label='delete?', locationcode='Delete+Frame',handler=onDeleteFrame) littleSizer.Add(frameDelete,0,WACV) mainSizer.Add(littleSizer,0,) G2frame.dataWindow.SetDataSize() if startScroll: # reset scroll to saved position G2frame.dataWindow.Scroll(0,startScroll) # set to saved scroll position wx.Yield()
################################################################################ ##### Stress/Strain ################################################################################
[docs]def UpdateStressStrain(G2frame,data): '''Shows and handles the controls on the "Stress/Strain" data tree entry ''' def OnAppendDzero(event): data['d-zero'].append({'Dset':1.0,'Dcalc':0.0,'pixLimit':10,'cutoff':1.0, 'ImxyObs':[[],[]],'ImtaObs':[[],[]],'ImtaCalc':[[],[]],'Emat':[1.0,1.0,1.0],'fixDset':False,'Ivar':0}) UpdateStressStrain(G2frame,data) def OnUpdateDzero(event): for item in data['d-zero']: if item['Dcalc']: #skip unrefined ones item['Dset'] = item['Dcalc'] UpdateStressStrain(G2frame,data) def OnCopyStrSta(event): Names = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',]) if len(Names) == 1: G2frame.ErrorDialog('Nothing to copy controls to','There must be more than one "IMG" pattern') return Source = G2frame.GPXtree.GetItemText(G2frame.Image) Names.pop(Names.index(Source)) dlg = G2G.G2MultiChoiceDialog(G2frame,'Copy stress/strain controls','Copy controls from '+Source+' to:',Names) try: if dlg.ShowModal() == wx.ID_OK: items = dlg.GetSelections() for item in items: name = Names[item] Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,name) CId = G2gd.GetGPXtreeItemId(G2frame,Id,'Stress/Strain') oldData = G2frame.GPXtree.GetItemPyData(CId) load = oldData.get('Sample load',0.0) Data = copy.deepcopy(data) Data['Sample load'] = load G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Stress/Strain'),Data) finally: dlg.Destroy() G2frame.GPXtree.SelectItem(G2frame.PickId) def OnLoadStrSta(event): pth = G2G.GetImportPath(G2frame) if not pth: pth = '.' dlg = wx.FileDialog(G2frame, 'Choose stress/strain file', pth, '', 'image control files (*.strsta)|*.strsta',wx.FD_OPEN) try: if dlg.ShowModal() == wx.ID_OK: filename = dlg.GetPath() File = open(filename,'r') S = File.read() data = eval(S) Controls = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.Image, 'Image Controls')) G2img.FitStrSta(G2frame.ImageZ,data,Controls) UpdateStressStrain(G2frame,data) G2plt.PlotExposedImage(G2frame,event=event) G2plt.PlotStrain(G2frame,data,newPlot=True) File.close() finally: dlg.Destroy() def OnSaveStrSta(event): pth = G2G.GetExportPath(G2frame) dlg = wx.FileDialog(G2frame, 'Choose stress/strain file', pth, '', 'image control files (*.strsta)|*.strsta',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT) try: if dlg.ShowModal() == wx.ID_OK: filename = dlg.GetPath() File = open(filename,'w') keys = ['Type','Sample phi','Sample z','Sample load'] keys2 = ['Dset','Dcalc','pixLimit','cutoff','Emat','fixDset'] File.write('{\n\t') for key in keys: if key in 'Type': File.write("'"+key+"':'"+data[key]+"',") else: File.write("'"+key+"':"+str(data[key])+',') File.write('\n\t'+"'d-zero':[\n") for data2 in data['d-zero']: File.write('\t\t{') for key in keys2: File.write("'"+key+"':"+str(data2[key])+',') File.write("'ImxyObs':[[],[]],'ImtaObs':[[],[]],'ImtaCalc':[[],[]]},\n") File.write('\t]\n}') File.close() finally: dlg.Destroy() def OnStrStaSample(event): filename = '' pth = G2G.GetImportPath(G2frame) if not pth: pth = '.' dlg = wx.FileDialog(G2frame, 'Choose multihistogram metadata text file', pth, '', 'metadata file (*.*)|*.*',wx.FD_OPEN) try: if dlg.ShowModal() == wx.ID_OK: filename = dlg.GetPath() File = open(filename,'r') S = File.readline() newItems = [] itemNames = [] Comments = [] while S: if S[0] == '#': Comments.append(S) S = File.readline() continue S = S.replace(',',' ').replace('\t',' ') Stuff = S[:-1].split() itemNames.append(Stuff[0]) newItems.append(Stuff[1:]) S = File.readline() File.close() finally: dlg.Destroy() if not filename: G2frame.ErrorDialog('Nothing to do','No file selected') return dataDict = dict(zip(itemNames,newItems)) ifany = False Names = [' ','Sample phi','Sample z','Sample load'] dlg = G2G.G2ColumnIDDialog( G2frame,' Choose multihistogram metadata columns:', 'Select columns',Comments,Names,np.array(newItems).T) try: if dlg.ShowModal() == wx.ID_OK: colNames,newData = dlg.GetSelection() dataDict = dict(zip(itemNames,newData.T)) for item in colNames: if item != ' ': ifany = True finally: dlg.Destroy() if not ifany: G2frame.ErrorDialog('Nothing to do','No columns identified') return histList = [] item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root) while item: name = G2frame.GPXtree.GetItemText(item) if name.startswith('IMG'): histList.append(name) item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie) colIds = {} for i,name in enumerate(colNames): if name != ' ': colIds[name] = i for hist in histList: name = hist.split()[1] #this is file name if name in dataDict: newItems = {} for item in colIds: newItems[item] = float(dataDict[name][colIds[item]]) Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,hist) stsrData = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Stress/Strain')) stsrData.update(newItems) UpdateStressStrain(G2frame,data) def OnPlotStrSta(event): Controls = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.Image, 'Image Controls')) RingInt = G2img.IntStrSta(G2frame.ImageZ,data,Controls) Names = ['d=%.3f'%(ring['Dcalc']) for ring in data['d-zero']] G2plt.PlotExposedImage(G2frame,event=event) G2frame.G2plotNB.Delete('Ring Intensities') G2plt.PlotXY(G2frame,RingInt,labelX='Azimuth', labelY='MRD',newPlot=True,Title='Ring Intensities', names=Names,lines=True) def OnSaveStrRing(event): Controls = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.Image, 'Image Controls')) RingInt = G2img.IntStrSta(G2frame.ImageZ,data,Controls) Names = ['d=%.3f'%(ring['Dcalc']) for ring in data['d-zero']] pth = G2G.GetExportPath(G2frame) dlg = wx.FileDialog(G2frame, 'Choose strain ring intensity file', pth, '', 'ring intensity file (*.txt)|*.txt',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT) try: if dlg.ShowModal() == wx.ID_OK: filename = dlg.GetPath() File = open(filename,'w') for i,name in enumerate(Names): File.write('%s%s\n'%(' Ring intensity for ',name)) File.write('%12s %12s\n'%('Azimuth','RMD')) for item in RingInt[i].T: File.write(' %12.3f %12.3f\n'%(item[0],item[1])) File.write('\n') File.close() finally: dlg.Destroy() def OnFitStrSta(event): Controls = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.Image, 'Image Controls')) G2img.FitStrSta(G2frame.ImageZ,data,Controls) print ('Strain fitting finished') UpdateStressStrain(G2frame,data) G2plt.PlotExposedImage(G2frame,event=event) G2plt.PlotStrain(G2frame,data,newPlot=True) def OnFitAllStrSta(event): choices = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',]) od = {'label_1':'Copy to next','value_1':False,'label_2':'Reverse order','value_2':False} dlg = G2G.G2MultiChoiceDialog(G2frame,'Stress/Strain fitting','Select images to fit:',choices,extraOpts=od) names = [] if dlg.ShowModal() == wx.ID_OK: for sel in dlg.GetSelections(): names.append(choices[sel]) Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Sequential strain fit results') if Id: SeqResult = G2frame.GPXtree.GetItemPyData(Id) else: SeqResult = {} Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text='Sequential strain fit results') SeqResult.update({'SeqPseudoVars':{},'SeqParFitEqList':[]}) else: dlg.Destroy() return dlg.Destroy() if not names: return dlg = wx.ProgressDialog('Sequential IMG Strain fit','Data set name = '+names[0],len(names), style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_REMAINING_TIME|wx.PD_CAN_ABORT) wx.BeginBusyCursor() goodnames = [] if od['value_2']: names.reverse() try: varyList = [] variables = [] for i,name in enumerate(names): print (' Sequential strain fit for '+name) dlg.Raise() GoOn = dlg.Update(i,newmsg='Data set name = '+name)[0] if not GoOn: break sId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,name) G2frame.Image = sId Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,sId, 'Image Controls')) StaCtrls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,sId, 'Stress/Strain')) if not len(StaCtrls['d-zero']): continue goodnames.append(name) Npix,imagefile,imagetag = G2frame.GPXtree.GetImageLoc(sId) image = GetImageZ(G2frame,Controls) sig = [] if i and od['value_1']: for j,ring in enumerate(StaCtrls['d-zero']): ring['Emat'] = copy.copy(variables[4*j:4*j+3]) varyList = [] variables = [] #get results from previous & put in StaCtrls G2img.FitStrSta(image,StaCtrls,Controls) G2plt.PlotStrain(G2frame,StaCtrls,newPlot=True) parmDict = {'Sample load':StaCtrls['Sample load'],} varyNames = ['e11','e12','e22'] Nvar = 5*len(StaCtrls['d-zero']) coVar = np.zeros((Nvar,Nvar)) for j,item in enumerate(StaCtrls['d-zero']): variables += item['Emat'] sig += item['Esig'] varylist = ['%d;%s'%(j,Name) for Name in varyNames] varyList += varylist parmDict.update(dict(zip(varylist,item['Emat']))) parmDict['%d;Dcalc'%(j)] = item['Dcalc'] variables.append(1.e6*(item['Dcalc']/item['Dset']-1.)) varyList.append('%d;h-mstrain'%(j)) sig.append(0) parmDict['%d;Ivar'%(j)] = item['Ivar'] variables.append(item['Ivar']) varyList.append('%d;Ivar'%(j)) sig.append(0) j4 = j*5 coVar[j4:j4+3,j4:j4+3] = item['covMat'] SeqResult[name] = {'variables':variables,'varyList':varyList,'sig':sig,'Rvals':[], 'covMatrix':coVar,'title':name,'parmDict':parmDict} else: SeqResult['histNames'] = goodnames dlg.Destroy() print (' ***** Sequential strain refinement successful *****') finally: wx.EndBusyCursor() SeqResult['histNames'] = choices G2frame.GPXtree.SetItemPyData(Id,SeqResult) G2frame.GPXtree.SelectItem(Id) print ('All images fitted') def SamSizer(): def OnStrainType(event): data['Type'] = strType.GetValue() samSizer = wx.FlexGridSizer(0,4,0,5) samSizer.Add(wx.StaticText(G2frame.dataWindow,-1,label=' Strain type: '),0,WACV) strType = wx.ComboBox(G2frame.dataWindow,value=data['Type'],choices=['True','Conventional'], style=wx.CB_READONLY|wx.CB_DROPDOWN) strType.SetValue(data['Type']) strType.Bind(wx.EVT_COMBOBOX, OnStrainType) samSizer.Add(strType,0,WACV) samSizer.Add(wx.StaticText(G2frame.dataWindow,-1,label=' Sample phi: '),0,WACV) samPhi = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'Sample phi',nDig=(10,3),typeHint=float,xmin=-360.,xmax=360.) samSizer.Add(samPhi,0,WACV) samSizer.Add(wx.StaticText(G2frame.dataWindow,-1,label=' Sample delta-z(mm): '),0,WACV) samZ = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'Sample z',nDig=(10,3),typeHint=float) samSizer.Add(samZ,0,WACV) samSizer.Add(wx.StaticText(G2frame.dataWindow,-1,label=' Sample load(MPa): '),0,WACV) samLoad = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'Sample load', nDig=[8,3],typeHint=float,) samSizer.Add(samLoad,0,WACV) return samSizer def DzeroSizer(): def OnStrainChange(event): # print (event) r,c = event.GetRow(),event.GetCol() if c == 0: data['d-zero'][r]['Dset'] = min(max(float(StrainGrid.GetCellValue(r,c)),0.25),20.) elif c == 1: data['d-zero'][r]['fixDset'] = bool(StrainGrid.GetCellValue(r,c)) elif c == 3: data['d-zero'][r]['cutoff'] = min(max(float(StrainGrid.GetCellValue(r,c)),0.5),20.) elif c == 4: data['d-zero'][r]['pixLimit'] = int(StrainGrid.GetCellValue(r,c)) elif c == 8: del data['d-zero'][r] StrainTable.DeleteRow(r) wx.CallAfter(UpdateStressStrain,G2frame,data) G2plt.PlotExposedImage(G2frame,event=event) G2plt.PlotStrain(G2frame,data,newPlot=True) def OnSetCol(event): c = event.GetCol() if c == 1: StrainGrid.ClearSelection() StrainGrid.SelectCol(c,True) choice = ['Y - set all','N - set none',] dlg = wx.SingleChoiceDialog(G2frame,'Select option for '+StrainGrid.GetColLabelValue(c-1), 'Strain controls',choice) dlg.CenterOnParent() if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() if sel == 0: for row in range(StrainGrid.GetNumberRows()): data['d-zero'][row]['fixDset']=True else: for row in range(StrainGrid.GetNumberRows()): data['d-zero'][row]['fixDset']=False wx.CallAfter(UpdateStressStrain,G2frame,data) colTypes = [wg.GRID_VALUE_FLOAT+':10,5',wg.GRID_VALUE_BOOL,wg.GRID_VALUE_FLOAT+':10,5',wg.GRID_VALUE_FLOAT+':10,1', wg.GRID_VALUE_CHOICE+':1,2,5,10,15,20',]+3*[wg.GRID_VALUE_FLOAT+':10,2',]+[wg.GRID_VALUE_BOOL,]+2*[wg.GRID_VALUE_FLOAT+':10,2',] colIds = ['d-zero','Poisson\n mean?','d-zero ave','I/Ib','nPix','e11','e12','e22','Delete?','h-mustrain','Ivar'] rowIds = [str(i) for i in range(len(data['d-zero']))] table = [[item['Dset'],item.get('fixDset',False),item['Dcalc'],item['cutoff'],item['pixLimit'], item['Emat'][0],item['Emat'][1],item['Emat'][2],False,1.e6*(item['Dcalc']/item['Dset']-1.),item['Ivar']] for item in data['d-zero']] StrainTable = G2G.Table(table,rowLabels=rowIds,colLabels=colIds,types=colTypes) StrainGrid = G2G.GSGrid(G2frame.dataWindow) StrainGrid.SetTable(StrainTable,True) StrainGrid.AutoSizeColumns(True) for r in range(len(data['d-zero'])): StrainGrid.SetCellStyle(r,2,VERY_LIGHT_GREY,True) StrainGrid.SetCellStyle(r,5,VERY_LIGHT_GREY,True) StrainGrid.SetCellStyle(r,6,VERY_LIGHT_GREY,True) StrainGrid.SetCellStyle(r,7,VERY_LIGHT_GREY,True) StrainGrid.SetCellStyle(r,9,VERY_LIGHT_GREY,True) StrainGrid.SetCellStyle(r,10,VERY_LIGHT_GREY,True) if 'phoenix' in wx.version(): StrainGrid.Bind(wg.EVT_GRID_CELL_CHANGED, OnStrainChange) else: StrainGrid.Bind(wg.EVT_GRID_CELL_CHANGE, OnStrainChange) StrainGrid.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK,OnSetCol) return StrainGrid # patches if 'Sample load' not in data: data['Sample load'] = 0.0 # end patches G2frame.dataWindow.ClearData() G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.StrStaMenu) G2frame.Bind(wx.EVT_MENU, OnAppendDzero, id=G2G.wxID_APPENDDZERO) G2frame.Bind(wx.EVT_MENU, OnUpdateDzero, id=G2G.wxID_UPDATEDZERO) G2frame.Bind(wx.EVT_MENU, OnFitStrSta, id=G2G.wxID_STRSTAFIT) G2frame.Bind(wx.EVT_MENU, OnPlotStrSta, id=G2G.wxID_STRSTAPLOT) G2frame.Bind(wx.EVT_MENU, OnSaveStrRing, id=G2G.wxID_STRRINGSAVE) G2frame.Bind(wx.EVT_MENU, OnFitAllStrSta, id=G2G.wxID_STRSTAALLFIT) G2frame.Bind(wx.EVT_MENU, OnCopyStrSta, id=G2G.wxID_STRSTACOPY) G2frame.Bind(wx.EVT_MENU, OnLoadStrSta, id=G2G.wxID_STRSTALOAD) G2frame.Bind(wx.EVT_MENU, OnSaveStrSta, id=G2G.wxID_STRSTASAVE) G2frame.Bind(wx.EVT_MENU, OnStrStaSample, id=G2G.wxID_STRSTSAMPLE) if G2frame.StrainKey == 'a': #probably doesn't happen G2frame.GetStatusBar().SetStatusText('Add strain ring active - LB pick d-zero value',1) else: G2frame.GetStatusBar().SetStatusText("To add strain data: On 2D Powder Image, key a:add ring",1) mainSizer = G2frame.dataWindow.GetSizer() mainSizer.Add((5,10),0) mainSizer.Add(SamSizer()) mainSizer.Add((5,10),0) mainSizer.Add(DzeroSizer()) G2frame.dataWindow.SetDataSize()
########################################################################### # Autointegration ###########################################################################
[docs]def ReadMask(filename): 'Read a mask (.immask) file' File = open(filename,'r') save = {} S = File.readline() while S: if S[0] == '#': S = File.readline() continue [key,val] = S.strip().split(':',1) if key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']: save[key] = eval(val) S = File.readline() File.close() CleanupMasks(save) return save
[docs]def ReadControls(filename): 'read an image controls (.imctrl) file' cntlList = ['wavelength','distance','tilt','invert_x','invert_y','type', 'fullIntegrate','outChannels','outAzimuths','LRazimuth','IOtth','azmthOff','DetDepth', 'calibskip','pixLimit','cutoff','calibdmin','Flat Bkg', 'PolaVal','SampleAbs','dark image','background image'] File = open(filename,'r') save = {} S = File.readline() while S: if S[0] == '#': S = File.readline() continue [key,val] = S.strip().split(':',1) if key in ['type','calibrant','binType','SampleShape',]: #strings save[key] = val elif key in ['rotation']: save[key] = float(val) elif key in ['center',]: if ',' in val: save[key] = eval(val) else: vals = val.strip('[] ').split() save[key] = [float(vals[0]),float(vals[1])] elif key in cntlList: save[key] = eval(val) S = File.readline() File.close() return save
[docs]def Read_imctrl(imctrl_file): '''Read an image control file and record control parms into a dict, with some simple type conversions ''' save = {'filename':imctrl_file} immask_file = os.path.splitext(imctrl_file)[0]+'.immask' if os.path.exists(immask_file): save['maskfile'] = immask_file else: save['maskfile'] = '(none)' cntlList = ['wavelength','distance','tilt','invert_x','invert_y','type', 'fullIntegrate','outChannels','outAzimuths','LRazimuth','IOtth','azmthOff','DetDepth', 'calibskip','pixLimit','cutoff','calibdmin','Flat Bkg', 'PolaVal','SampleAbs','dark image','background image','setdist'] File = open(imctrl_file,'r') fullIntegrate = False try: S = File.readline() while S: if S[0] == '#': S = File.readline() continue [key,val] = S.strip().split(':',1) if val.find(':') != -1: #print 'rejecting ',key,val S = File.readline() continue if key in ['type','calibrant','binType','SampleShape',]: #strings save[key] = val elif key == 'rotation': save[key] = float(val) elif key == 'fullIntegrate': fullIntegrate = eval(val) elif key == 'LRazimuth': vals = eval(val) save['LRazimuth_min'] = float(vals[0]) save['LRazimuth_max'] = float(vals[1]) elif key == 'IOtth': save['IOtth_min'],save['IOtth_max'] = eval(val)[0:2] elif key == 'center': if ',' in val: vals = eval(val) else: vals = val.strip('[] ').split() vals = [float(vals[0]),float(vals[1])] save['center_x'],save['center_y'] = vals[0:2] elif key in cntlList: save[key] = eval(val) S = File.readline() finally: File.close() if fullIntegrate: save['LRazimuth_min'],save['LRazimuth_max'] = 0.,360. return save
[docs]class AutoIntFrame(wx.Frame): '''Creates a wx.Frame window for the Image AutoIntegration. The intent is that this will be used as a non-modal dialog window. Implements a Start button that morphs into a pause and resume button. This button starts a processing loop that is repeated every :meth:`PollTime` seconds. :param wx.Frame G2frame: main GSAS-II frame :param float PollTime: frequency in seconds to repeat calling the processing loop. (Default is 30.0 seconds.) ''' def __init__(self,G2frame,PollTime=30.0): def OnStart(event): '''Called when the start button is pressed. Changes button label to Pause. When Pause is pressed the label changes to Resume. When either Start or Resume is pressed, the processing loop is started. When Pause is pressed, the loop is stopped. ''' # check inputs for errors before starting #err = '' #if not any([self.params[fmt] for fmt in self.fmtlist]): # err += '\nPlease select at least one output format\n' #if err: # G2G.G2MessageBox(self,err) # return self.Pause = False # change button label if self.btnstart.GetLabel() != 'Pause': self.btnstart.SetLabel('Pause') self.Status.SetStatusText('Press Pause to delay integration or Reset to prepare to reintegrate all images') if self.timer.IsRunning(): self.timer.Stop() self.PreventReEntryTimer = False if self.StartLoop(): G2G.G2MessageBox(self,'Error in setting up integration. See console') return self.OnTimerLoop(None) # run once immediately if not self.Pause: # no pause, so start timer to check for new files self.timer.Start(int(1000*PollTime),oneShot=False) return # we will get to this point if Paused self.OnPause() def OnReset(event): '''Called when Reset button is pressed. This stops the processing loop and resets the list of integrated files so all images can be reintegrated. ''' self.btnstart.SetLabel('Restart') self.Status.SetStatusText('Press Restart to reload and re-integrate images matching filter') if self.timer.IsRunning(): self.timer.Stop() self.Reset = True self.Pause = True def OnQuit(event): '''Stop the processing loop and close the Frame ''' if self.timer.IsRunning(): self.timer.Stop() # make sure we stop first wx.CallAfter(self.Destroy) def OnBrowse(event): '''Responds when the Browse button is pressed to load a file. The routine determines which button was pressed and gets the appropriate file type and loads it into the appropriate place in the dict. ''' if btn3 == event.GetEventObject(): dlg = wx.DirDialog( self, 'Select directory for output files', self.params['outdir'],wx.DD_DEFAULT_STYLE) dlg.CenterOnParent() try: if dlg.ShowModal() == wx.ID_OK: self.params['outdir'] = dlg.GetPath() fInp3.SetValue(self.params['outdir']) finally: dlg.Destroy() return elif btn4 == event.GetEventObject(): msg = '' pth = G2G.GetExportPath(G2frame) dlg = wx.FileDialog( self, 'Select a PDF parameter file', pth, self.params['pdfprm'], "PDF controls file (*.pdfprm)|*.pdfprm", wx.FD_OPEN | wx.FD_FILE_MUST_EXIST) dlg.CenterOnParent() try: if dlg.ShowModal() == wx.ID_OK: self.params['pdfprm'] = dlg.GetPath() fInp4.SetValue(self.params['pdfprm']) scanPDFprm() msg = self.checkPDFprm(True) finally: dlg.Destroy() if 'Error' in msg: print(msg) lbl = 'PDFPRM error' else: msg = 'Information from file {}\n\n{}'.format(self.params['pdfprm'],msg) lbl = 'PDFPRM information' G2G.G2MessageBox(self,msg,lbl) return def OnRadioSelect(event): '''Respond to a radiobutton selection and when in table mode, get distance-dependent parameters from user. ''' self.Evaluator = None if self.useTable.GetValue(): dlg = None try: dlg = IntegParmTable(self) # create the dialog dlg.CenterOnParent() if dlg.ShowModal() == wx.ID_OK: self.ImgTblParms = dlg.parms self.IMfileList = dlg.IMfileList self.Evaluator = DefineEvaluator(dlg) self.params['Mode'] = 'table' self.editTable.Enable(True) else: self.useActive.SetValue(True) finally: if dlg: dlg.Destroy() elif self.useActive.GetValue(): self.params['Mode'] = 'active' self.imageBase = G2frame.Image self.useActive.SetLabel("Active Image: "+ G2frame.GPXtree.GetItemText(self.imageBase)) self.editTable.Enable(False) else: print('unexpected mode in OnRadioSelect') def OnEditTable(event): '''Called to edit the distance-dependent parameter look-up table. Should be called only when table is defined and active. ''' dlg = None try: dlg = IntegParmTable(self,self.ImgTblParms,self.IMfileList) dlg.CenterOnParent() if dlg.ShowModal() == wx.ID_OK: self.ImgTblParms = dlg.parms self.IMfileList = dlg.IMfileList self.Evaluator = DefineEvaluator(dlg) self.params['Mode'] = 'table' self.editTable.Enable(True) else: self.useActive.SetValue(True) self.params['Mode'] = 'active' self.imageBase = G2frame.Image self.useActive.SetLabel("Active Image: "+ G2frame.GPXtree.GetItemText(self.imageBase)) self.editTable.Enable(False) finally: if dlg: dlg.Destroy() def showPDFctrls(event): '''Called to show or hide AutoPDF widgets. Note that fInp4 must be included in the sizer layout with .Show(True) before .Show(False) will work properly. ''' fInp4.Enable(self.params['ComputePDF']) fInp4.Show(self.params['ComputePDF']) fInp4a.Enable(self.params['ComputePDF']) btn4.Enable(self.params['ComputePDF']) cOpt.Enable(self.params['ComputePDF']) if self.params['ComputePDF']: lbl4.SetForegroundColour("black") lbl4a.SetForegroundColour("black") else: lbl4.SetForegroundColour("gray") lbl4a.SetForegroundColour("gray") def scanPDFprm(**kw): fInp4.invalid = not os.path.exists(fInp4.GetValue()) fInp4._IndicateValidity() def OnAutoScale(event): self.AutoScale = autoscale.GetValue() def OnAutoScaleName(event): self.AutoScaleName = scalename.GetValue() self.Scale[0] = self.AutoScales[self.AutoScaleName] scaleval.SetValue(self.Scale[0]) ################################################## # beginning of __init__ processing ################################################## self.G2frame = G2frame self.ImgTblParms = None self.IMfileList = None self.Evaluator = None self.params = {} self.Reset = False self.Pause = False self.PreventReEntryShowMatch = False self.PreventReEntryTimer = False self.params['IMGfile'] = '' self.params['MaskFile'] = '' self.params['IgnoreMask'] = True self.fmtlist = G2IO.ExportPowderList(G2frame) self.timer = wx.Timer() self.timer.Bind(wx.EVT_TIMER,self.OnTimerLoop) self.imageBase = G2frame.Image self.params['ComputePDF'] = False self.params['pdfDmax'] = 0.0 self.params['pdfprm'] = '' self.params['optPDF'] = True self.pdfControls = {} self.AutoScale = False self.Scale = [1.0,] G2frame.GPXtree.GetSelection() size,imagefile,imagetag = G2frame.GPXtree.GetImageLoc(self.imageBase) self.params['readdir'],fileroot = os.path.split(imagefile) self.params['filter'] = '*'+os.path.splitext(fileroot)[1] self.params['outdir'] = os.path.abspath(self.params['readdir']) Comments = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId( G2frame,self.imageBase, 'Comments')) DefaultAutoScaleNames = GSASIIpath.GetConfigValue('Autoscale_ParmNames') self.AutoScaleName = GSASIIpath.GetConfigValue('DefaultAutoScale') self.AutoScales = {} if DefaultAutoScaleNames is not None: for comment in Comments: if '=' in comment: name,val = comment.split('=',1) if name in DefaultAutoScaleNames: try: self.AutoScales[name] = float(val) if name == self.AutoScaleName: self.Scale[0] = float(val) except ValueError: continue wx.Frame.__init__(self, G2frame, title='Automatic Integration', style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX) self.Status = self.CreateStatusBar() self.Status.SetStatusText('Press Start to load and integrate images matching filter') mnpnl = wx.Panel(self) mnsizer = wx.BoxSizer(wx.VERTICAL) # box for integration controls & masks input lbl = wx.StaticBox(mnpnl, wx.ID_ANY, "Integration Control") lblsizr = wx.StaticBoxSizer(lbl, wx.VERTICAL) lblsizr.Add(wx.StaticText(mnpnl, wx.ID_ANY,'Use integration parameters from:')) self.useActive = wx.RadioButton(mnpnl, wx.ID_ANY, style = wx.RB_GROUP) self.useActive.Bind(wx.EVT_RADIOBUTTON, OnRadioSelect) self.useActive.SetLabel("Active Image: "+G2frame.GPXtree.GetItemText(self.imageBase)) lblsizr.Add(self.useActive,0,wx.EXPAND,1) self.useActive.SetValue(True) minisizer = wx.BoxSizer(wx.HORIZONTAL) self.useTable = wx.RadioButton(mnpnl, wx.ID_ANY, "From distance look-up table") minisizer.Add(self.useTable,0,wx.ALIGN_LEFT|wx.ALL,1) self.useTable.Bind(wx.EVT_RADIOBUTTON, OnRadioSelect) self.editTable = wx.Button(mnpnl, wx.ID_ANY, "Edit table") minisizer.Add(self.editTable,0,wx.ALIGN_LEFT,10) self.editTable.Enable(False) self.editTable.Bind(wx.EVT_BUTTON, OnEditTable) # bind button and deactivate be default lblsizr.Add(minisizer) mnsizer.Add(lblsizr,0,wx.EXPAND,0) # file filter stuff sizer = wx.BoxSizer(wx.HORIZONTAL) sizer.Add(wx.StaticText(mnpnl, wx.ID_ANY,'Read images from ')) self.readDir = G2G.ValidatedTxtCtrl(mnpnl,self.params,'readdir', OnLeave=self.ShowMatchingFiles,size=(200,-1)) sizer.Add(self.readDir,1,wx.EXPAND,1) btn3 = wx.Button(mnpnl, wx.ID_ANY, "Browse") btn3.Bind(wx.EVT_BUTTON, self.SetSourceDir) sizer.Add(btn3,0,wx.ALIGN_RIGHT|WACV) mnsizer.Add(sizer,0,wx.EXPAND,0) # not yet implemented sizer = wx.BoxSizer(wx.HORIZONTAL) sizer.Add(wx.StaticText(mnpnl, wx.ID_ANY,'Keep read images in tree ')) self.params['keepReadImage'] = True keepImage = G2G.G2CheckBox(mnpnl,'',self.params,'keepReadImage') sizer.Add(keepImage) keepImage.Enable(False) sizer.Add((-1,-1),1,wx.EXPAND,1) sizer.Add(wx.StaticText(mnpnl, wx.ID_ANY,' Image filter')) flterInp = G2G.ValidatedTxtCtrl(mnpnl,self.params,'filter', OnLeave=self.ShowMatchingFiles) sizer.Add(flterInp) mnsizer.Add(sizer,0,wx.EXPAND,0) self.ListBox = wx.ListBox(mnpnl,size=(-1,100)) mnsizer.Add(self.ListBox,1,wx.EXPAND,1) self.ShowMatchingFiles(self.params['filter']) # box for output selections lbl = wx.StaticBox(mnpnl, wx.ID_ANY, "Output settings") lblsizr = wx.StaticBoxSizer(lbl, wx.VERTICAL) sizer = wx.BoxSizer(wx.HORIZONTAL) sizer.Add(wx.StaticText(mnpnl, wx.ID_ANY,'Write to: '),0,WACV) fInp3 = G2G.ValidatedTxtCtrl(mnpnl,self.params,'outdir',notBlank=False,size=(300,-1)) sizer.Add(fInp3,1,wx.EXPAND) btn3 = wx.Button(mnpnl, wx.ID_ANY, "Browse") btn3.Bind(wx.EVT_BUTTON, OnBrowse) sizer.Add(btn3,0,wx.ALIGN_RIGHT|WACV) lblsizr.Add(sizer,0,wx.EXPAND) sizer = wx.BoxSizer(wx.HORIZONTAL) sizer.Add(wx.StaticText(mnpnl, wx.ID_ANY,'Select format(s):')) # format choice selection usedfmt = [] self.multipleFmtChoices = {} for dfmt in sorted(self.fmtlist[0]): sizer.Add((6,2)) # add a bit of extra space fmt = dfmt[1:] self.params[fmt] = False if fmt in usedfmt: # is extension used more than once self.multipleFmtChoices[fmt] = None else: usedfmt.append(fmt) btn = G2G.G2CheckBox(mnpnl,dfmt,self.params,fmt, OnChange=self.TestInput) sizer.Add(btn) lblsizr.Add(sizer) sizer = wx.BoxSizer(wx.HORIZONTAL) sizer.Add(wx.StaticText(mnpnl, wx.ID_ANY,'Separate dir for each format: ')) self.params['SeparateDir'] = False sizer.Add(G2G.G2CheckBox(mnpnl,'',self.params,'SeparateDir')) lblsizr.Add(sizer) if self.AutoScales: sizer = wx.BoxSizer(wx.HORIZONTAL) autoscale = wx.CheckBox(mnpnl,label='Do autoscaling with:') autoscale.Bind(wx.EVT_CHECKBOX,OnAutoScale) sizer.Add(autoscale,0,WACV) scalename = wx.ComboBox(mnpnl,value=self.AutoScaleName,choices=list(self.AutoScales.keys()), style=wx.CB_READONLY|wx.CB_DROPDOWN) scalename.Bind(wx.EVT_COMBOBOX,OnAutoScaleName) sizer.Add(scalename,0,WACV) sizer.Add(wx.StaticText(mnpnl,label=' to '),0,WACV) scaleval = G2G.ValidatedTxtCtrl(mnpnl,self.Scale,0,nDig=(10,2),xmin=1.) sizer.Add(scaleval,0,WACV) lblsizr.Add(sizer,0) #ToDO: Autonormalize, parm name?, scaling value? sizer = wx.BoxSizer(wx.HORIZONTAL) sizer.Add(wx.StaticText(mnpnl, wx.ID_ANY,'Autocompute PDF:'),0,WACV) sizer.Add(G2G.G2CheckBox(mnpnl,'',self.params,'ComputePDF',OnChange=showPDFctrls)) lbl4a = wx.StaticText(mnpnl, wx.ID_ANY,'Max detector distance: ') sizer.Add(lbl4a,0,WACV) fInp4a = G2G.ValidatedTxtCtrl(mnpnl,self.params,'pdfDmax',xmin=0.0) sizer.Add(fInp4a,0,WACV) cOpt = G2G.G2CheckBox(mnpnl,'Optimize',self.params,'optPDF') sizer.Add(cOpt) lblsizr.Add(sizer,0) sizer = wx.BoxSizer(wx.HORIZONTAL) lbl4 = wx.StaticText(mnpnl, wx.ID_ANY,'PDF control: ') sizer.Add(lbl4,0,WACV) fInp4 = G2G.ValidatedTxtCtrl(mnpnl,self.params,'pdfprm',notBlank=True,size=(300,-1), OnLeave=scanPDFprm) sizer.Add(fInp4,1,wx.EXPAND) btn4 = wx.Button(mnpnl, wx.ID_ANY, "Browse") btn4.Bind(wx.EVT_BUTTON, OnBrowse) sizer.Add(btn4,0,wx.ALIGN_RIGHT|WACV) lblsizr.Add(sizer,0,wx.EXPAND) mnsizer.Add(lblsizr,0,wx.EXPAND,1) # buttons on bottom mnsizer.Add(wx.StaticText(mnpnl, wx.ID_ANY,'AutoIntegration controls'),0,wx.TOP,5) sizer = wx.BoxSizer(wx.HORIZONTAL) sizer.Add((20,-1)) self.btnstart = wx.Button(mnpnl, wx.ID_ANY, "Start") self.btnstart.Bind(wx.EVT_BUTTON, OnStart) sizer.Add(self.btnstart) self.btnreset = wx.Button(mnpnl, wx.ID_ANY, "Reset") self.btnreset.Bind(wx.EVT_BUTTON, OnReset) sizer.Add(self.btnreset) sizer.Add((20,-1),wx.EXPAND,1) self.btnclose = wx.Button(mnpnl, wx.ID_ANY, "Close") self.btnclose.Bind(wx.EVT_BUTTON, OnQuit) sizer.Add(self.btnclose) sizer.Add((20,-1)) mnsizer.Add(sizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP,5) # finish up window mnpnl.SetSizer(mnsizer) OnRadioSelect(None) # disable widgets mnsizer.Fit(self) self.CenterOnParent() self.Show() showPDFctrls(None) def TestInput(self,event): for fmt in self.multipleFmtChoices: if not self.params[fmt]: continue if self.multipleFmtChoices[fmt]: continue choices = [] for f,l in zip(self.fmtlist[0],self.fmtlist[1]): if f[1:] == fmt: choices.append(l) if len(choices) < 2: print('Error: why no choices in TestInput?') return # select the format here dlg = G2G.G2SingleChoiceDialog(self, 'There is more than one format with a '+ '.{} output. Choose the one to use'.format(fmt), 'Choose output format',choices) dlg.clb.SetSelection(0) # force a selection if dlg.ShowModal() == wx.ID_OK and dlg.GetSelection() >= 0: self.multipleFmtChoices[fmt] = choices[dlg.GetSelection()] dlg.Destroy() else: dlg.Destroy() return
[docs] def checkPDFprm(self,ShowContents=False): '''Read in the PDF (.pdfprm) parameter file and check for problems. If ShowContents is True, a formatted text version of some of the file contents is returned. If errors are found, the return string will contain the string "Error:" at least once. ''' self.pdfControls = {} msg = '' File = None try: File = open(self.params['pdfprm'],'r') S = File.readline() while S: if '#' in S: S = File.readline() continue key,val = S.split(':',1) try: self.pdfControls[key] = eval(val) except: self.pdfControls[key] = val S = File.readline() except Exception as err: msg += 'PDF Processing Error: error with open or read of {}'.format(self.params['pdfprm']) if GSASIIpath.GetConfigValue('debug'): print('DBG_'+msg) print('DBG_'+err) self.pdfControls = {} return msg finally: if File: File.close() formula = '' for el in self.pdfControls['ElList']: if self.pdfControls['ElList'][el]['FormulaNo'] <= 0: continue if formula: formula += ' ' formula += '{}({:.1f})'.format(el,self.pdfControls['ElList'][el]['FormulaNo']) if not formula: msg += 'Error: no chemical formula in file' for key in ['Sample Bkg.','Container','Container Bkg.']: if key not in self.pdfControls: if msg: msg += '\n' msg += 'Error: missing key in self.pdfControls: '+key continue if msg or not ShowContents: return msg # stop on error msg += 'Default formula: '+formula+'\n' for key in ['Sample Bkg.','Container','Container Bkg.']: name = self.pdfControls[key]['Name'] mult = self.pdfControls[key].get('Mult',0.0) if not name: continue msg += '\n{}: {:.2f} * "{}"'.format(key,mult,name) if not G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,name): msg += ' *** missing ***' return msg
[docs] def SetSourceDir(self,event): '''Use a dialog to get a directory for image files ''' dlg = wx.DirDialog(self, 'Select directory for image files', self.params['readdir'],wx.DD_DEFAULT_STYLE) dlg.CenterOnParent() try: if dlg.ShowModal() == wx.ID_OK: self.params['readdir'] = dlg.GetPath() self.readDir.SetValue(self.params['readdir']) self.ShowMatchingFiles(None) finally: dlg.Destroy() return
[docs] def ShowMatchingFiles(self,value,invalid=False,**kwargs): '''Find and show images in the tree and the image files matching the image file directory (self.params['readdir']) and the image file filter (self.params['filter']) and add this information to the GUI list box ''' G2frame = self.G2frame if invalid: return msg = '' if self.PreventReEntryShowMatch: return self.PreventReEntryShowMatch = True imageFileList = [] for img in G2gd.GetGPXtreeDataNames(G2frame,['IMG ']): imgId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,img) size,imagefile,imagetag = G2frame.GPXtree.GetImageLoc(imgId) if imagefile not in imageFileList: imageFileList.append(imagefile) if img not in G2frame.IntegratedList: if msg: msg += '\n' msg += ' ' + img if msg: msg = "Loaded images to integrate:\n" + msg + "\n" msg1 = "" try: if os.path.exists(self.params['readdir']): imageList = sorted( glob.glob(os.path.join(self.params['readdir'],self.params['filter']))) if not imageList: msg1 = 'Warning: No files match search string '+os.path.join(self.params['readdir'],self.params['filter']) else: for fil in imageList: if fil not in imageFileList: msg1 += '\n '+fil if msg1: msg += 'Files to integrate from '+os.path.join(self.params['readdir'],self.params['filter'])+msg1 else: msg += 'No files found to read in '+self.params['readdir'] else: msg += 'Warning: does not exist: '+self.params['readdir'] except IndexError: msg += 'Error searching for files named '+os.path.join(self.params['readdir'],self.params['filter']) self.ListBox.Clear() self.ListBox.AppendItems(msg.split('\n')) self.PreventReEntryShowMatch = False return
[docs] def OnPause(self): '''Respond to Pause, changes text on button/Status line, if needed Stops timer self.Pause should already be True ''' if self.timer.IsRunning(): self.timer.Stop() if self.btnstart.GetLabel() == 'Restart': return if self.btnstart.GetLabel() != 'Resume': print('\nPausing autointegration\n') self.btnstart.SetLabel('Resume') self.Status.SetStatusText( 'Press Resume to continue integration or Reset to prepare to reintegrate all images') self.Pause = True
[docs] def IntegrateImage(self,img,useTA=None,useMask=None): '''Integrates a single image. Ids for created PWDR entries (more than one is possible) are placed in G2frame.IntgOutList ''' G2frame = self.G2frame imgId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,img) G2frame.Image = imgId G2frame.PickId = G2gd.GetGPXtreeItemId(G2frame,G2frame.Image, 'Image Controls') # do integration size,imagefile,imagetag = G2frame.GPXtree.GetImageLoc(imgId) if self.AutoScale: Comments = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId( G2frame,imgId, 'Comments')) for comment in Comments: if '=' in comment: name,val = comment.split('=',1) if name == self.AutoScaleName: val = float(val) if val > 0.: Scale = self.Scale[0]/val break masks = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.Image, 'Masks')) data = G2frame.GPXtree.GetItemPyData(G2frame.PickId) # simulate a Image Controls press, since that is where the # integration is hidden UpdateImageControls(G2frame,data,masks,useTA=useTA,useMask=useMask,IntegrateOnly=True) G2frame.IntegratedList.append(img) # note this as integrated # split name and control number try: s = re.split(r'(\d+)\Z',os.path.split(os.path.splitext(imagefile)[0])[1]) except AttributeError: # not sure why, but sometimes imagefile is a list here (should not be)! s = re.split(r'(\d+)\Z',os.path.split(os.path.splitext(imagefile[0])[0])[1]) namepre = s[0] if len(s) > 1: namenum = s[1] else: namenum = '' for Id in G2frame.IntgOutList: # loop over newly created PWDR entry(ies) # save the created PWDR tree names so that a reset can delete them G2frame.Image = Id treename = G2frame.GPXtree.GetItemText(Id) G2frame.AutointPWDRnames.append(treename) # write out the images in the selected formats Sdata = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Sample Parameters')) if self.AutoScale: print ('Rescale by %.4f'%(Scale)) y,w = G2frame.GPXtree.GetItemPyData(Id)[1][1:3] y *= Scale w /= Scale**2 # determine the name for the current file fileroot = namepre if len(G2frame.IntgOutList) > 1: fileroot += "_AZM" if 'Azimuth' in Sdata: fileroot += str(int(10*Sdata['Azimuth'])) fileroot += "_" fileroot += namenum # loop over selected formats for fmt in self.params: if not self.params[fmt]: continue if '.'+fmt not in self.fmtlist[0]: continue if self.params['SeparateDir']: subdir = fmt else: subdir = '' hint = '' if self.multipleFmtChoices.get(fmt): hint = self.multipleFmtChoices.get(fmt) fil = os.path.join(self.params['outdir'],subdir,fileroot) G2IO.ExportPowder(G2frame,treename,fil+'.x','.'+fmt,hint=hint) # dummy extension (.x) is replaced before write)
[docs] def EnableButtons(self,flag): '''Relabels and enable/disables the buttons at window bottom when auto-integration is running ''' # for unclear reasons disabling these buttons causes OnRadioSelect to be invoked # on windows if sys.platform != "win32": for item in (self.btnstart,self.btnreset,self.btnclose): item.Enable(flag) self.btnstart.SetLabel('Pause') wx.Yield()
[docs] def ResetFromTable(self,dist): '''Sets integration parameters based on values from the lookup table ''' #dist = self.controlsDict['distance'] interpDict,imgctrl,immask = self.Evaluator(dist) # interpolated calibration values if GSASIIpath.GetConfigValue('debug'): print ('DBG_interpolated values: ',interpDict) self.ImageControls = ReadControls(imgctrl) self.ImageControls.update(interpDict) self.ImageControls['showLines'] = True self.ImageControls['ring'] = [] self.ImageControls['rings'] = [] self.ImageControls['ellipses'] = [] self.ImageControls['setDefault'] = False for i in 'range','size','GonioAngles': if i in self.ImageControls: del self.ImageControls[i] # load copy of Image Masks if immask: self.ImageMasks = ReadMask(immask) if list(self.ImageMasks['Thresholds'][0]) == self.ImageMasks['Thresholds'][1]: #avoid copy of unchanged thresholds del self.ImageMasks['Thresholds'] else: self.ImageMasks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[], 'SpotMask':{'esdMul':3.,'spotMask':None},}
[docs] def StartLoop(self): '''Prepare to start autointegration timer loop. Save current Image params for use in future integrations also label the window so users understand what is being used ''' print('\nStarting new autointegration\n') G2frame = self.G2frame # show current IMG base if self.params['Mode'] != 'table': self.useActive.SetLabel("Active Image: "+ G2frame.GPXtree.GetItemText(self.imageBase)) # load copy of Image Controls from current image and clean up # items that should not be copied self.ImageControls = copy.deepcopy( G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId( G2frame,self.imageBase, 'Image Controls'))) self.ImageControls['showLines'] = True self.ImageControls['ring'] = [] self.ImageControls['rings'] = [] self.ImageControls['ellipses'] = [] self.ImageControls['setDefault'] = False del self.ImageControls['range'] del self.ImageControls['size'] del self.ImageControls['GonioAngles'] # load copy of Image Masks, keep thresholds self.ImageMasks = copy.deepcopy( G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,self.imageBase, 'Masks'))) self.Thresholds = self.ImageMasks['Thresholds'][:] if list(self.Thresholds[0]) == self.Thresholds[1]: #avoid copy of unchanged thresholds del self.ImageMasks['Thresholds'] # make sure all output directories exist if self.params['SeparateDir']: for dfmt in self.fmtlist[0]: if not self.params[dfmt[1:]]: continue dir = os.path.join(self.params['outdir'],dfmt[1:]) if not os.path.exists(dir): os.makedirs(dir) else: if not os.path.exists(self.params['outdir']): os.makedirs(self.params['outdir']) if self.Reset: # special things to do after Reset has been pressed self.G2frame.IntegratedList = [] if self.params['Mode'] != 'table': # reset controls and masks for all IMG items in tree to master for img in G2gd.GetGPXtreeDataNames(G2frame,['IMG ']): # update controls from master controlsDict = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,self.imageBase, 'Image Controls')) controlsDict.update(self.ImageControls) # update masks from master ImageMasks = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,self.imageBase, 'Masks')) ImageMasks.update(self.ImageMasks) # delete all PWDR items created after last Start was pressed idlist = [] item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root) while item: itemName = G2frame.GPXtree.GetItemText(item) if itemName in G2frame.AutointPWDRnames: idlist.append(item) item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie) for item in idlist: G2frame.GPXtree.Delete(item) wx.Yield() self.Reset = False G2frame.AutointPWDRnames = [] # list of created PWDR tree item names G2frame.AutointPDFnames = [] # list of created PWDR tree item names # check that AutoPDF input is OK, offer chance to use alternate PWDRs if referenced ones # are not present if self.params['ComputePDF']: msg = self.checkPDFprm() if 'Error:' in msg: print(msg) return True fileList = [] Id, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root) while Id: name = G2frame.GPXtree.GetItemText(Id) if name.startswith('PWDR '): fileList.append(name) Id, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie) if not fileList: print(msg) print('No PWDR entries to select') return True for key in ['Sample Bkg.','Container','Container Bkg.']: name = self.pdfControls[key]['Name'] if not name: continue if not G2gd.GetGPXtreeItemId(G2frame,G2frame.root,name): indx = G2G.ItemSelector(fileList, self, header='Select PWDR item', title='Select a PWDR tree item for '+key+'\n(or cancel to quit)') if indx is None: print('No PWDR entry selected for '+key) return True self.pdfControls[key]['Name'] = fileList[indx] return False
[docs] def OnTimerLoop(self,event): '''A method that is called every :meth:`PollTime` seconds that is used to check for new files and process them. Integrates new images. Also optionally sets up and computes PDF. This is called only after the "Start" button is pressed (then its label reads "Pause"). ''' def AutoIntegrateImage(imgId,useTA=None,useMask=None): '''Integrates an image that has been read into the data tree and updates the AutoInt window. ''' img = G2frame.GPXtree.GetItemText(imgId) controlsDict = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,imgId, 'Image Controls')) ImageMasks = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,imgId, 'Masks')) if self.params['Mode'] == 'table': # look up parameter values from table useTA = None #force remake of x,y-->2th,azm map self.ResetFromTable(controlsDict['setdist']) # update controls from master controlsDict.update(self.ImageControls) # update masks from master w/o Thresholds ImageMasks.update(self.ImageMasks) self.EnableButtons(False) try: self.IntegrateImage(img,useTA=useTA,useMask=useMask) finally: self.EnableButtons(True) self.G2frame.oldImagefile = '' # mark image as changed; reread as needed wx.Yield() self.ShowMatchingFiles(self.params['filter']) wx.Yield() def AutoComputePDF(imgId): '''Computes a PDF for a PWDR data tree tree item ''' for pwdr in G2frame.AutointPWDRnames[:]: if not pwdr.startswith('PWDR '): continue if pwdr in G2frame.AutointPDFnames: continue PWid = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,pwdr) controlsDict = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,imgId, 'Image Controls')) if self.params['pdfDmax'] != 0 and controlsDict['distance'] > self.params['pdfDmax']: print('Skipping PDF for '+pwdr+' due to detector position') continue # Setup PDF Data = G2frame.GPXtree.GetItemPyData(PWid)[1] pwdrMin = np.min(Data[1]) Parms = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId( G2frame,PWid,'Instrument Parameters'))[0] fullLimits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId( G2frame,PWid,'Limits'))[0] if 'C' in Parms['Type'][0]: qMax = tth2q(fullLimits[1],G2mth.getWave(Parms)) else: qMax = tof2q(fullLimits[0],Parms['difC'][1]) Qlimits = [0.9*qMax,qMax] item = pwdr Comments = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId( G2frame,imgId, 'Comments')) ElList = {} sumnum = 1.0 for item in Comments: #grab chemical formula from Comments, if there if 'formula' in item[:15].lower(): formula = item.split('=')[1].split() elems = formula[::2] nums = formula[1::2] formula = zip(elems,nums) sumnum = 0. for [elem,num] in formula: ElData = G2elem.GetElInfo(elem,Parms) ElData['FormulaNo'] = float(num) sumnum += float(num) ElList[elem] = ElData PDFnames = G2gd.GetGPXtreeDataNames(G2frame,['PDF ',]) PDFid = G2obj.CreatePDFitems(G2frame,pwdr,ElList.copy(),Qlimits,sumnum,pwdrMin,PDFnames) if not PDFid: continue PDFdata = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId( G2frame,PDFid, 'PDF Controls')) PDFdata.update(copy.deepcopy(self.pdfControls)) if ElList: PDFdata['ElList'] = ElList # override with formula from comments, if present PDFdata['Sample']['Name'] = pwdr # compute PDF wx.Yield() G2pdG.computePDF(G2frame,PDFdata) wx.Yield() G2frame.PatternId = PDFid G2plt.PlotISFG(G2frame,PDFdata,newPlot=False,plotType='G(R)') if self.params['optPDF']: G2pdG.OptimizePDF(G2frame,PDFdata,maxCycles=10,) wx.Yield() G2plt.PlotISFG(G2frame,PDFdata,newPlot=False,plotType='G(R)') G2frame.AutointPDFnames.append(pwdr) # save names of PDF entry to be deleted later if needed G2frame.AutointPWDRnames.append(G2frame.GPXtree.GetItemText(PDFid)) G2frame = self.G2frame try: self.currImageList = sorted( glob.glob(os.path.join(self.params['readdir'],self.params['filter']))) self.ShowMatchingFiles(self.params['filter']) except IndexError: self.currImageList = [] return if self.PreventReEntryTimer: return self.PreventReEntryTimer = True imageFileList = [] # integrate the images that have already been read in, but # have not yet been processed oldData = {'tilt':0.,'distance':0.,'rotation':0.,'center':[0.,0.],'DetDepth':0.,'azmthOff':0.} oldMhash = 0 if 'useTA' not in dir(self): #initial definition; reuse if after Resume self.useTA = None self.useMask = None for img in G2gd.GetGPXtreeDataNames(G2frame,['IMG ']): imgId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,img) size,imagefile,imagetag = G2frame.GPXtree.GetImageLoc(imgId) # Create a list of image files that have been read in if imagefile not in imageFileList: imageFileList.append(imagefile) # skip if already integrated if img in G2frame.IntegratedList: continue Data = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,imgId, 'Image Controls')) sameTA = True for item in ['tilt','distance','rotation','center','DetDepth','azmthOff']: if Data[item] != oldData[item]: sameTA = False if not sameTA: t0 = time.time() self.useTA = G2img.MakeUseTA(Data,blkSize) print(' Use new image controls; xy->th,azm mtime: %.3f'%(time.time()-t0)) Mask = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,imgId, 'Masks')) Mhash = copy.deepcopy(Mask) Mhash.pop('Thresholds') Mhash = hash(str(Mhash)) if Mhash != oldMhash: t0 = time.time() self.useMask = G2img.MakeUseMask(Data,Mask,blkSize) print(' Use new mask; make mask time: %.3f'%(time.time()-t0)) oldMhash = Mhash AutoIntegrateImage(imgId,self.useTA,self.useMask) oldData = Data if self.pdfControls: AutoComputePDF(imgId) self.Pause |= G2frame.PauseIntegration if self.Pause: self.OnPause() self.PreventReEntryTimer = False self.Raise() return # loop over image files matching glob, reading in any new ones if self.useTA is None or self.useMask is None: print('Integration will not be fast; there is no beginning image controls') #TODO: work this out?? for newImage in self.currImageList: if newImage in imageFileList or self.Pause: continue # already read? for imgId in G2IO.ReadImages(G2frame,newImage): AutoIntegrateImage(imgId,self.useTA,self.useMask) if self.pdfControls: AutoComputePDF(imgId) self.Pause |= G2frame.PauseIntegration if self.Pause: self.OnPause() self.PreventReEntryTimer = False self.Raise() return if GSASIIpath.GetConfigValue('debug'): import datetime print ("DBG_Timer tick at {:%d %b %Y %H:%M:%S}\n".format(datetime.datetime.now())) self.PreventReEntryTimer = False self.Raise()
[docs]def DefineEvaluator(dlg): '''Creates a function that provides interpolated values for a given distance value ''' def Evaluator(dist): '''Interpolate image parameters for a supplied distance value :param float dist: distance to use for interpolation :returns: a list with 3 items: * a dict with interpolated parameter values, * the closest imctrl and * the closest maskfile (or None) ''' x = np.array([float(i) for i in parms[0]]) closest = abs(x-dist).argmin() D = {'setdist':dist} imctfile = IMfileList[closest] if parms[-1][closest].lower() != '(none)': maskfile = parms[-1][closest] else: maskfile = None for c in range(1,cols-1): lbl = ParmList[c] if lbl in nonInterpVars: if lbl in ['outChannels',]: D[lbl] = int(float(parms[c][closest])) else: D[lbl] = float(parms[c][closest]) else: y = np.array([float(i) for i in parms[c]]) D[lbl] = np.interp(dist,x,y) # full integration when angular range is 0 D['fullIntegrate'] = (D['LRazimuth_min'] == D['LRazimuth_max']) # conversion for paired values for a,b in ('center_x','center_y'),('LRazimuth_min','LRazimuth_max'),('IOtth_min','IOtth_max'): r = a.split('_')[0] D[r] = [D[a],D[b]] if r in ['LRazimuth',]: D[r] = [int(D[a]),int(D[b])] del D[a] del D[b] return D,imctfile,maskfile # save local copies of values needed in Evaluator parms = dlg.ReadImageParmTable() IMfileList = dlg.IMfileList cols = dlg.list.GetColumnCount() ParmList = dlg.ParmList nonInterpVars = dlg.nonInterpVars return Evaluator
[docs]class IntegParmTable(wx.Dialog): '''Creates a dialog window with a table of integration parameters. :meth:`ShowModal` will return wx.ID_OK if the process has been successful. In this case, :func:`DefineEvaluator` should be called to obtain a function that creates a dictionary with interpolated parameter values. ''' ParmList = ('setdist','distance','center_x','center_y','wavelength','tilt','rotation','DetDepth', 'LRazimuth_min','LRazimuth_max','IOtth_min','IOtth_max','outChannels', 'maskfile', ) nonInterpVars = ('tilt','rotation','LRazimuth_min','LRazimuth_max','IOtth_min','IOtth_max', 'outChannels') # values in this list are taken from nearest rather than interpolated HeaderList = ('Set Dist','Calib Dist','X cntr','Y cntr','wavelength','tilt','rotation','DetDepth', 'Azimuth min','Azimuth max','2Th min','2Th max','Int. pts', 'Mask File', ) def __init__(self,parent,parms=None,IMfileList=None,readFileList=None): self.G2frame = parent.G2frame dlg = None pth = '' wx.Dialog.__init__(self,parent,style=wx.RESIZE_BORDER|wx.DEFAULT_DIALOG_STYLE) if readFileList: self.parms,self.IMfileList = self.ReadFiles(readFileList) elif parms: self.parms = parms # list of values by column self.IMfileList = IMfileList # list of .imctrl file names for each entry in table else: self.parms = [] # list of values by column self.IMfileList = [] # list of .imctrl file names for each entry in table files = [] try: pth = G2G.GetImportPath(self.G2frame) if not pth: pth = '.' dlg = wx.FileDialog(parent, 'Read previous table or build new table by selecting image control files', pth, style=wx.FD_OPEN| wx.FD_MULTIPLE, wildcard='Integration table (*.imtbl)|*.imtbl|image control files (.imctrl)|*.imctrl') dlg.CenterOnParent() if dlg.ShowModal() == wx.ID_OK: files = dlg.GetPaths() self.parms,self.IMfileList = self.ReadFiles(files) finally: if dlg: dlg.Destroy() if not files: wx.CallAfter(self.EndModal,wx.ID_CANCEL) return mainSizer = wx.BoxSizer(wx.VERTICAL) self.list = ImgIntLstCtrl(self, wx.ID_ANY,style=wx.LC_REPORT| wx.BORDER_SUNKEN) mainSizer.Add(self.list,1,wx.EXPAND,1) btnsizer = wx.BoxSizer(wx.HORIZONTAL) btn = wx.Button(self, wx.ID_OK) btnsizer.Add(btn) btn = wx.Button(self, wx.ID_ANY,'Save as file') btn.Bind(wx.EVT_BUTTON,self._onSave) btnsizer.Add(btn) btn = wx.Button(self, wx.ID_CLOSE,'Quit') btn.Bind(wx.EVT_BUTTON,self._onClose) btnsizer.Add(btn) mainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER|wx.ALL, 5) self.SetSizer(mainSizer) self.list.FillList(self.parms)
[docs] def ReadFiles(self,files): '''Reads a list of .imctrl files or a single .imtbl file ''' tmpDict = {} if not files: return # option 1, a dump from a previous save if os.path.splitext(files[0])[1] == '.imtbl': fp = open(files[0],'r') S = fp.readline() while S: if S[0] != '#': [key,val] = S[:-1].split(':',1) tmpDict[key] = eval(val) S = fp.readline() fp.close() # delete entries where files do not exist m1 = [i for i,f in enumerate(tmpDict['filenames']) if not os.path.exists(f)] if m1: print('\nimctrl file not found:') for i in m1: print('\t#'+str(i)+': '+tmpDict['filenames'][i]) m2 = [i for i,f in enumerate(tmpDict['maskfile']) if not (os.path.exists(f) or f.startswith('('))] if m2: print('\nmask file not found') for i in m2: print('\t#'+str(i)+': '+tmpDict['maskfile'][i]) m3 = [i for i,d in enumerate(tmpDict['distance']) if d < 0] if m3: print('\nDropping entries due to negative distance: '+str(m3)) m = sorted(set(m1 + m2 + m3)) m.reverse() for c in m: for key in tmpDict: del tmpDict[key][c] fileList = tmpDict.get('filenames','[]') parms = [] if 'setdist' not in tmpDict: print(u'Old file, recreate before using: {}'.format(files[0])) return [[]],[] for key in self.ParmList: try: float(tmpDict[key][0]) parms.append([str(G2py3.FormatSigFigs(val1,sigfigs=5)) for val1 in tmpDict[key]]) except ValueError: parms.append(tmpDict[key]) except IndexError: print('No valid image control entries read') wx.CallAfter(self.EndModal,wx.ID_CANCEL) return [[]],[] return parms,fileList # option 2, read in a list of files for file in files: # read all files; place in dict by distance imgDict = Read_imctrl(file) dist = imgDict.get('setdist',imgDict['distance']) if dist is None: print('Skipping old file, redo: {}'.format(file)) tmpDict[dist] = imgDict parms = [[] for key in self.ParmList] fileList = [] for d in sorted(tmpDict): fileList.append(tmpDict[d].get('filename')) if d is None: continue if d < 0: continue for i,key in enumerate(self.ParmList): val = tmpDict[d].get(key) try: val = str(G2py3.FormatSigFigs(val,sigfigs=5)) except: val = str(val) parms[i].append(val) return parms,fileList
[docs] def ReadImageParmTable(self): '''Reads possibly edited values from the ListCtrl table and returns a list of values for each column. ''' rows = self.list.GetItemCount() cols = self.list.GetColumnCount() parms = [] for c in range(cols): parms.append([]) for r in range(rows): parms[c].append(self.list.GetItem(r,c).GetText()) return parms
def _onClose(self,event): 'Called when Cancel button is pressed' self.EndModal(wx.ID_CANCEL) def _onSave(self,event): 'Called when save button is pressed; creates a .imtbl file' fil = '' if self.G2frame.GSASprojectfile: fil = os.path.splitext(self.G2frame.GSASprojectfile)[0]+'.imtbl' dir,f = os.path.split(fil) pth = G2G.GetExportPath(self.G2frame) try: dlg = wx.FileDialog(self, 'Save table data as', defaultDir=pth, defaultFile=f, style=wx.SAVE, wildcard='G2 Image Param Table file (*.imtbl)|*.imtbl') dlg.CenterOnParent() if dlg.ShowModal() != wx.ID_OK: return fil = dlg.GetPath() fil = os.path.splitext(fil)[0]+'.imtbl' finally: dlg.Destroy() parms = self.ReadImageParmTable() print('Writing image parameter table as '+fil) fp = open(fil,'w') for c in range(len(parms)-1): lbl = self.ParmList[c] fp.write(lbl+': '+str([eval(i) for i in parms[c]])+'\n') lbl = self.ParmList[c+1] fp.write(lbl+': '+str(parms[c+1])+'\n') lbl = 'filenames' fp.write(lbl+': '+str(self.IMfileList)+'\n') fp.close()
[docs]class ImgIntLstCtrl(wx.ListCtrl, listmix.ListCtrlAutoWidthMixin,listmix.TextEditMixin): '''Creates a custom ListCtrl for editing Image Integration parameters ''' def __init__(self, parent, ID, pos=wx.DefaultPosition,size=(1000,200),style=0): self.parent=parent wx.ListCtrl.__init__(self, parent, ID, pos, size, style) listmix.ListCtrlAutoWidthMixin.__init__(self) listmix.TextEditMixin.__init__(self) self.Bind(wx.EVT_LEFT_DCLICK, self.OnDouble) #self.Bind(wx.EVT_LIST_COL_CLICK, self.OnColClick)
[docs] def FillList(self,parms): 'Places the current parms into the table' # the use of InsertStringItem and SetStringItem are depricated in 4.0 but # I am not quite sure how to replace them with InsertItem and SetItem yet. # Perhaps switch to ULC.UltimateListCtrl? # maxint = 2**31-1 self.ClearAll() self.rowlen = len(self.parent.ParmList) for i,lbl in enumerate(self.parent.HeaderList): self.InsertColumn(i, lbl) for r,d in enumerate(parms[0]): if d is None: continue if d == 'None': continue if float(d) < 0: continue index = self.InsertStringItem(maxint, d) for j in range(1,len(parms)): self.SetStringItem(index, j, parms[j][r]) for i,lbl in enumerate(self.parent.ParmList): self.SetColumnWidth(i, wx.LIST_AUTOSIZE)
[docs] def OnDouble(self,evt): 'respond to a double-click' self.CloseEditor() fil = '(none)' pth = G2G.GetImportPath(self.parent.G2frame) if not pth: pth = '.' try: dlg = wx.FileDialog(self, 'Select mask or control file to add (Press cancel if none)', pth, style=wx.FD_OPEN,wildcard='Add GSAS-II mask file (.immask)|*.immask|add image control file (.imctrl)|*.imctrl') dlg.CenterOnParent() if dlg.ShowModal() == wx.ID_OK: fil = dlg.GetPath() finally: dlg.Destroy() if os.path.splitext(fil)[1] != '.imctrl': self.SetStringItem(self.curRow, self.rowlen-1, fil) self.SetColumnWidth(self.rowlen-1, wx.LIST_AUTOSIZE) else: # insert or overwrite an instrument parameter set if not os.path.exists(fil): print('Does not exist: '+fil) return imgDict = Read_imctrl(fil) dist = imgDict['distance'] parms = self.parent.ReadImageParmTable() x = np.array([float(i) for i in parms[0]]) closest = abs(x-dist).argmin() closeX = x[closest] # fix IMfileList for c,lbl in enumerate(self.parent.ParmList): try: vali = G2py3.FormatSigFigs(float(imgDict[lbl]),sigfigs=5) except ValueError: vali = imgDict[lbl] if abs(closeX-dist) < 1.: # distance is within 1 mm, replace parms[c][closest] = vali elif dist > closeX: # insert after parms[c].insert(closest+1,vali) else: parms[c].insert(closest,vali) if abs(closeX-dist) < 1.: # distance is within 1 mm, replace self.parent.IMfileList[closest] = fil elif dist > closeX: # insert after self.parent.IMfileList.insert(closest+1,fil) else: self.parent.IMfileList.insert(closest,fil) self.FillList(parms)
# Autointegration end ###########################################################################
[docs]def testColumnMetadata(G2frame): '''Test the column-oriented metadata parsing, as implemented at 1-ID, by showing results when using a .par and .lbls pair. * Select a .par file, if more than one in selected dir. * Select the .*lbls file, if more than one matching .par file. * Parse the .lbls file, showing errors if encountered; loop until errors are fixed. * Search for an image or a line in the .par file and show the results when interpreted See :func:`GSASIIfiles.readColMetadata` for more details. ''' if not GSASIIpath.GetConfigValue('Column_Metadata_directory'): G2G.G2MessageBox(G2frame,'The configuration option for I-ID Metadata is not set.\n'+ 'Please use the File/Preferences menu to set Column_Metadata_directory', 'Warning') return parFiles = glob.glob(os.path.join(GSASIIpath.GetConfigValue('Column_Metadata_directory'),'*.par')) if not parFiles: G2G.G2MessageBox(G2frame,'No .par files found in directory {}. ' .format(GSASIIpath.GetConfigValue('Column_Metadata_directory'))+ '\nThis is set by config variable Column_Metadata_directory '+ '(Set in File/Preferences menu).', 'Warning') return parList = [] for parFile in parFiles: lblList = [] parRoot = os.path.splitext(parFile)[0] for f in glob.glob(parRoot+'.*lbls'): if os.path.exists(f): lblList.append(f) if not len(lblList): continue parList.append(parFile) if len(parList) == 0: G2G.G2MessageBox(G2frame,'No .lbls or .EXT_lbls file found for .par file(s) in directory {}. ' .format(GSASIIpath.GetConfigValue('Column_Metadata_directory'))+ '\nThis is set by config variable Column_Metadata_directory '+ '(Set in File/Preferences menu).', 'Warning') return elif len(parList) == 1: parFile = parList[0] else: dlg = G2G.G2SingleChoiceDialog(G2frame, 'More than 1 .par file found. (Better if only 1!). Choose the one to test in '+ GSASIIpath.GetConfigValue('Column_Metadata_directory'), 'Choose .par file', [os.path.split(i)[1] for i in parList]) if dlg.ShowModal() == wx.ID_OK: parFile = parList[dlg.GetSelection()] dlg.Destroy() else: dlg.Destroy() return # got .par file; now work on .*lbls file lblList = [] parRoot = os.path.splitext(parFile)[0] for f in glob.glob(parRoot+'.*lbls'): if os.path.exists(f): lblList.append(f) if not len(lblList): raise Exception('How did this happen! No .*lbls files for '+parFile) elif len(lblList) == 1: lblFile = lblList[0] else: dlg = G2G.G2SingleChoiceDialog(G2frame, 'Select label file for .par file '+parFile, 'Choose label file', [os.path.split(i)[1] for i in lblList]) if dlg.ShowModal() == wx.ID_OK: lblFile = lblList[dlg.GetSelection()] dlg.Destroy() else: dlg.Destroy() return # parse the labels file errors = True while errors: labels,lbldict,keyCols,keyExp,errors = G2fil.readColMetadataLabels(lblFile) if errors: t = "Error reading file "+lblFile for l in errors: t += '\n' t += l t += "\n\nPlease edit the file and press OK (or Cancel to quit)" dlg = wx.MessageDialog(G2frame,message=t, caption="Read Error",style=wx.ICON_ERROR| wx.OK|wx.STAY_ON_TOP|wx.CANCEL) if dlg.ShowModal() != wx.ID_OK: return # request a line number, read that line dlg = G2G.SingleStringDialog(G2frame,'Read what', 'Enter a line number or an image file name (-1=last line)', '-1',size=(400,-1)) if dlg.Show(): fileorline = dlg.GetValue() dlg.Destroy() else: dlg.Destroy() return # and report the generated key pairs in metadata dict linenum = None try: linenum = int(fileorline) except: imageName = os.path.splitext(os.path.split(fileorline)[1])[0] fp = open(parFile,'r') for iline,line in enumerate(fp): if linenum is not None: if iline == linenum: items = line.strip().split(' ') n = "Line {}".format(iline) break else: continue else: items = line.strip().split(' ') nameList = keyExp['filename'](*[items[j] for j in keyCols['filename']]) if type(nameList) is str: if nameList != imageName: continue name = nameList break else: for name in nameList: print (name,name == imageName) if name == imageName: n = "Image {} found in line {}".format(imageName,iline) break # got a match else: continue break else: if linenum is not None: n = "Line {}".format(iline) else: n = "Image {} not found. Reporting line {}".format(imageName,iline) items = line.strip().split(' ') fp.close() metadata = G2fil.evalColMetadataDicts(items,labels,lbldict,keyCols,keyExp,True) title = "Results: ("+n+")" t = ['Files: '+parFile,lblFile,' '] n = ["Named parameters:"] l = ['',"Labeled columns:"] for key in sorted(metadata): if key == "filename" or key.startswith('label_prm'): continue if key in keyCols: n += [" {} = {}".format(key,metadata[key])] elif key in lbldict.values(): l += [" {} = {}".format(key,metadata[key])] else: t += ["** Unexpected: {}".format(key,metadata[key])] if type(metadata['filename']) is str: l += ["","Filename: "+ metadata['filename']] else: l += ["","Filename(s): "] for i,j in enumerate(metadata['filename']): if i: l[-1] += ', ' l[-1] += j t += n + l + ['','Unused columns:'] usedCols = list(lbldict.keys()) for i in keyCols.values(): usedCols += i for i in range(len(items)): if i in usedCols: continue t += [" {}: {}".format(i,items[i])] dlg = G2G.G2SingleChoiceDialog(None,title,'Column metadata parse results',t, monoFont=True,filterBox=False,size=(400,600), style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER|wx.CENTRE|wx.OK) dlg.ShowModal()