Source code for GSASIIIO

# -*- coding: utf-8 -*-
########### SVN repository information ###################
# $Date: 2021-06-21 22:58:24 +0000 (Mon, 21 Jun 2021) $
# $Author: toby $
# $Revision: 4968 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASIIIO.py $
# $Id: GSASIIIO.py 4968 2021-06-21 22:58:24Z toby $
########### SVN repository information ###################
'''
*GSASIIIO: Misc I/O routines*
=============================

Module with miscellaneous routines for input and output. Many
are GUI routines to interact with user.

Includes support for image reading.

Also includes base class for data export routines (TODO: should move)

TODO: This module needs some work to separate wx from non-wx routines. GUI 
routines should probably move to GSASIIctrlGUI.
'''

from __future__ import division, print_function

# Allow this to be imported without wx present. Was needed for G2scriptable, but is
# likely not needed anymore
try:
    import wx
except ImportError:
    # was needed by sphinx, but probably not anymore
    class Placeholder(object):
        def __init__(self):
            self.Dialog = object
    wx = Placeholder()
import math
import numpy as np
import numpy.ma as ma

import copy
import platform
if '2' in platform.python_version_tuple()[0]:
    import cPickle
else:
    import pickle as cPickle
import sys
import re
import random as ran
import GSASIIpath
GSASIIpath.SetVersionNumber("$Revision: 4968 $")
try:
    import GSASIIdataGUI as G2gd
except ImportError:
    pass
import GSASIIobj as G2obj
import GSASIIlattice as G2lat
try:
    import GSASIIpwdGUI as G2pdG
    import GSASIIimgGUI as G2imG
except ImportError:
    pass
import GSASIIElem as G2el
import GSASIIstrIO as G2stIO
import GSASIImapvars as G2mv
import GSASIIfiles as G2fil
try:
    import GSASIIctrlGUI as G2G
except ImportError:
    pass
import os
import os.path as ospath

DEBUG = False       #=True for various prints
TRANSP = False      #=true to transpose images for testing
if GSASIIpath.GetConfigValue('Transpose'): TRANSP = True
npsind = lambda x: np.sin(x*np.pi/180.)

[docs]def sfloat(S): 'Convert a string to float. An empty field or a unconvertable value is treated as zero' if S.strip(): try: return float(S) except ValueError: pass return 0.0
[docs]def sint(S): 'Convert a string to int. An empty field is treated as zero' if S.strip(): return int(S) else: return 0
[docs]def trim(val): '''Simplify a string containing leading and trailing spaces as well as newlines, tabs, repeated spaces etc. into a shorter and more simple string, by replacing all ranges of whitespace characters with a single space. :param str val: the string to be simplified :returns: the (usually) shortened version of the string ''' return re.sub('\\s+', ' ', val).strip()
[docs]def FileDlgFixExt(dlg,file): 'this is needed to fix a problem in linux wx.FileDialog' ext = dlg.GetWildcard().split('|')[2*dlg.GetFilterIndex()+1].strip('*') if ext not in file: file += ext return file
[docs]def GetPowderPeaks(fileName): 'Read powder peaks from a file' sind = lambda x: math.sin(x*math.pi/180.) asind = lambda x: 180.*math.asin(x)/math.pi wave = 1.54052 File = open(fileName,'r') Comments = [] peaks = [] S = File.readline() while S: if S[:1] == '#': Comments.append(S[:-1]) else: item = S.split() if len(item) == 1: peaks.append([float(item[0]),1.0]) elif len(item) > 1: peaks.append([float(item[0]),float(item[0])]) S = File.readline() File.close() if Comments: print ('Comments on file:') for Comment in Comments: print (Comment) if 'wavelength' in Comment: wave = float(Comment.split('=')[1]) Peaks = [] if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa for peak in peaks: dsp = peak[0] sth = wave/(2.0*dsp) if sth < 1.0: tth = 2.0*asind(sth) else: break Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0]) else: #2-thetas - assume Cuka (for now) for peak in peaks: tth = peak[0] dsp = wave/(2.0*sind(tth/2.0)) Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0]) limits = [1000.,0.] for peak in Peaks: limits[0] = min(limits[0],peak[0]) limits[1] = max(limits[1],peak[0]) limits[0] = max(1.,(int(limits[0]-1.)/5)*5.) limits[1] = min(170.,(int(limits[1]+1.)/5)*5.) return Comments,Peaks,limits,wave
[docs]def GetCheckImageFile(G2frame,treeId): '''Try to locate an image file if the project and image have been moved together. If the image file cannot be found, request the location from the user. :param wx.Frame G2frame: main GSAS-II Frame and data object :param wx.Id treeId: Id for the main tree item for the image :returns: Npix,imagefile,imagetag with (Npix) number of pixels, imagefile, if it exists, or the name of a file that does exist or False if the user presses Cancel and (imagetag) an optional image number ''' Npix,Imagefile,imagetag = G2frame.GPXtree.GetImageLoc(treeId) if isinstance(Imagefile,list): imagefile,imagetag = Imagefile else: imagefile = Imagefile if not os.path.exists(imagefile): print ('Image file '+imagefile+' not found') fil = imagefile.replace('\\','/') # windows?! # see if we can find a file with same name or in a similarly named sub-dir pth,fil = os.path.split(fil) prevpth = None while pth and pth != prevpth: prevpth = pth if os.path.exists(os.path.join(G2frame.dirname,fil)): print ('found image file '+os.path.join(G2frame.dirname,fil)) imagefile = os.path.join(G2frame.dirname,fil) G2frame.GPXtree.UpdateImageLoc(treeId,imagefile) return Npix,imagefile,imagetag pth,enddir = os.path.split(pth) fil = os.path.join(enddir,fil) # not found as a subdirectory, drop common parts of path for last saved & image file names # if image was .../A/B/C/imgs/ima.ge # & GPX was .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1 # will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls')) gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files imgPath = imagefile.replace('\\','/').split('/') for p1,p2 in zip(gpxPath,imgPath): if p1 == p2: gpxPath.pop(0),imgPath.pop(0) else: break fil = os.path.join(*imgPath) # file with non-common prefix elements prevpth = None pth = os.path.abspath(G2frame.dirname) while pth and pth != prevpth: prevpth = pth if os.path.exists(os.path.join(pth,fil)): print ('found image file '+os.path.join(pth,fil)) imagefile = os.path.join(pth,fil) G2frame.GPXtree.UpdateImageLoc(treeId,imagefile) return Npix,imagefile,imagetag pth,enddir = os.path.split(pth) #GSASIIpath.IPyBreak() if not os.path.exists(imagefile): # note that this fails (at least on Mac) to get an image during the GUI initialization prevnam = os.path.split(imagefile)[1] prevext = os.path.splitext(imagefile)[1] wildcard = 'Image format (*'+prevext+')|*'+prevext dlg = wx.FileDialog(G2frame, 'Previous image file ('+prevnam+') not found; open here', '.', prevnam, wildcard,wx.FD_OPEN) try: dlg.SetFilename(''+ospath.split(imagefile)[1]) if dlg.ShowModal() == wx.ID_OK: imagefile = dlg.GetPath() G2frame.GPXtree.UpdateImageLoc(treeId,imagefile) else: imagefile = None # was False finally: dlg.Destroy() return Npix,imagefile,imagetag
def EditImageParms(parent,Data,Comments,Image,filename): dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters', style=wx.DEFAULT_DIALOG_STYLE | wx.RESIZE_BORDER) def onClose(event): dlg.EndModal(wx.ID_OK) mainsizer = wx.BoxSizer(wx.VERTICAL) h,w = Image.size[:2] mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)), 0,wx.ALIGN_LEFT|wx.ALL, 2) vsizer = wx.BoxSizer(wx.HORIZONTAL) vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '), 0,wx.ALIGN_LEFT|wx.ALL, 2) wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength') vsizer.Add(wdgt) mainsizer.Add(vsizer,0,wx.ALIGN_LEFT|wx.ALL, 2) vsizer = wx.BoxSizer(wx.HORIZONTAL) vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '), 0,wx.ALIGN_LEFT|wx.ALL, 2) wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,size=(50,-1)) vsizer.Add(wdgt) vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),wx.ALIGN_LEFT|wx.ALL, 2) wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,size=(50,-1)) vsizer.Add(wdgt) mainsizer.Add(vsizer,0,wx.ALIGN_LEFT|wx.ALL, 2) vsizer = wx.BoxSizer(wx.HORIZONTAL) vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '), 0,wx.ALIGN_LEFT|wx.ALL, 2) wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance') vsizer.Add(wdgt) mainsizer.Add(vsizer,0,wx.ALIGN_LEFT|wx.ALL, 2) vsizer = wx.BoxSizer(wx.HORIZONTAL) vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '), 0,wx.ALIGN_LEFT|wx.ALL, 2) wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,size=(75,-1)) vsizer.Add(wdgt) vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),wx.ALIGN_LEFT|wx.ALL, 2) wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,size=(75,-1)) vsizer.Add(wdgt) mainsizer.Add(vsizer,0,wx.ALIGN_LEFT|wx.ALL, 2) vsizer = wx.BoxSizer(wx.HORIZONTAL) vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '), 0,wx.ALIGN_LEFT|wx.ALL, 2) wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1)) vsizer.Add(wdgt) mainsizer.Add(vsizer,0,wx.ALIGN_LEFT|wx.ALL, 2) btnsizer = wx.StdDialogButtonSizer() OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue') OKbtn.SetDefault() OKbtn.Bind(wx.EVT_BUTTON,onClose) btnsizer.AddButton(OKbtn) # not sure why this is needed btnsizer.Realize() mainsizer.Add(btnsizer, 1, wx.ALL|wx.EXPAND, 5) dlg.SetSizer(mainsizer) dlg.CenterOnParent() dlg.ShowModal()
[docs]def LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image): '''Load an image into the tree. Saves the location of the image, as well as the ImageTag (where there is more than one image in the file), if defined. ''' ImgNames = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',]) TreeLbl = 'IMG '+os.path.basename(imagefile) ImageTag = Data.get('ImageTag') if ImageTag: TreeLbl += ' #'+'%04d'%(ImageTag) imageInfo = (imagefile,ImageTag) else: imageInfo = imagefile TreeName = G2obj.MakeUniqueLabel(TreeLbl,ImgNames) Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=TreeName) G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments) Imax = np.amax(Image) if G2frame.imageDefault: Data.update(copy.deepcopy(G2frame.imageDefault)) Data['showLines'] = True Data['ring'] = [] Data['rings'] = [] Data['cutoff'] = 10. Data['pixLimit'] = 20 Data['edgemin'] = 100000000 Data['calibdmin'] = 0.5 Data['calibskip'] = 0 Data['ellipses'] = [] Data['calibrant'] = '' Data['GonioAngles'] = [0.,0.,0.] Data['DetDepthRef'] = False else: Data['type'] = 'PWDR' Data['color'] = GSASIIpath.GetConfigValue('Contour_color','Paired') if 'tilt' not in Data: #defaults if not preset in e.g. Bruker importer Data['tilt'] = 0.0 Data['rotation'] = 0.0 Data['pixLimit'] = 20 Data['calibdmin'] = 0.5 Data['cutoff'] = 10. Data['showLines'] = False Data['calibskip'] = 0 Data['ring'] = [] Data['rings'] = [] Data['edgemin'] = 100000000 Data['ellipses'] = [] Data['GonioAngles'] = [0.,0.,0.] Data['DetDepth'] = 0. Data['DetDepthRef'] = False Data['calibrant'] = '' Data['IOtth'] = [5.0,50.0] if GSASIIpath.GetConfigValue('Image_2theta_min'): try: Data['IOtth'][0] = float(GSASIIpath.GetConfigValue('Image_2theta_min')) except: pass if GSASIIpath.GetConfigValue('Image_2theta_max'): try: Data['IOtth'][1] = float(GSASIIpath.GetConfigValue('Image_2theta_max')) except: pass Data['LRazimuth'] = [0.,180.] Data['azmthOff'] = 0.0 Data['outChannels'] = 2500 Data['outAzimuths'] = 1 Data['centerAzm'] = False Data['fullIntegrate'] = GSASIIpath.GetConfigValue('fullIntegrate',True) Data['setRings'] = False Data['background image'] = ['',-1.0] Data['dark image'] = ['',-1.0] Data['Flat Bkg'] = 0.0 Data['Oblique'] = [0.5,False] Data['setDefault'] = False Data['range'] = [(0,Imax),[0,Imax]] G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Image Controls'),Data) Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[], 'Thresholds':[(0,Imax),[0,Imax]], 'SpotMask':{'esdMul':3.,'spotMask':None}} G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Masks'),Masks) G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Stress/Strain'), {'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0}) G2frame.GPXtree.SetItemPyData(Id,[Npix,imageInfo]) G2frame.PickId = Id G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId) G2frame.Image = Id
[docs]def GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None,FormatName=''): '''Read a single image with an image importer. This is called to reread an image after it has already been imported with :meth:`GSASIIdataGUI.GSASII.OnImportGeneric` (or :func:`ReadImages` in Auto Integration) so it is not necessary to reload metadata. :param wx.Frame G2frame: main GSAS-II Frame and data object. :param str imagefile: name of image file :param bool imageOnly: If True return only the image, otherwise (default) return more (see below) :param int/str ImageTag: specifies a particular image to be read from a file. First image is read if None (default). :param str formatName: the image reader formatName :returns: an image as a numpy array or a list of four items: Comments, Data, Npix and the Image, as selected by imageOnly ''' # determine which formats are compatible with this file primaryReaders = [] secondaryReaders = [] for rd in G2frame.ImportImageReaderlist: flag = rd.ExtensionValidator(imagefile) if flag is None: secondaryReaders.append(rd) elif flag: if not FormatName: primaryReaders.append(rd) elif FormatName in rd.formatName: #This is a kluge because the rd.formatName was changed! primaryReaders.append(rd) if len(secondaryReaders) + len(primaryReaders) == 0: print('Error: No matching format for file '+imagefile) raise Exception('No image read') errorReport = '' if not imagefile: return for rd in primaryReaders+secondaryReaders: rd.ReInitialize() # purge anything from a previous read rd.errors = "" # clear out any old errors if not rd.ContentsValidator(imagefile): # rejected on cursory check errorReport += "\n "+rd.formatName + ' validator error' if rd.errors: errorReport += ': '+rd.errors continue if imageOnly: ParentFrame = None # prevent GUI access on reread else: ParentFrame = G2frame if GSASIIpath.GetConfigValue('debug'): flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag) else: flag = False try: flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag) except rd.ImportException as detail: rd.errors += "\n Read exception: "+str(detail) except Exception as detail: import traceback rd.errors += "\n Unhandled read exception: "+str(detail) rd.errors += "\n Traceback info:\n"+str(traceback.format_exc()) if flag: # this read succeeded if rd.Image is None: raise Exception('No image read. Strange!') if GSASIIpath.GetConfigValue('Transpose'): print ('Transposing Image!') rd.Image = rd.Image.T #rd.readfilename = imagefile if imageOnly: return rd.Image else: return rd.Comments,rd.Data,rd.Npix,rd.Image else: print('Error reading file '+imagefile) print('Error messages(s)\n'+errorReport) raise Exception('No image read')
[docs]def ReadImages(G2frame,imagefile): '''Read one or more images from a file and put them into the Tree using image importers. Called only in :meth:`AutoIntFrame.OnTimerLoop`. ToDo: Images are most commonly read in :meth:`GSASIIdataGUI.GSASII.OnImportGeneric` which is called from :meth:`GSASIIdataGUI.GSASII.OnImportImage` it would be good if these routines used a common code core so that changes need to be made in only one place. :param wx.Frame G2frame: main GSAS-II Frame and data object. :param str imagefile: name of image file :returns: a list of the id's of the IMG tree items created ''' # determine which formats are compatible with this file primaryReaders = [] secondaryReaders = [] for rd in G2frame.ImportImageReaderlist: flag = rd.ExtensionValidator(imagefile) if flag is None: secondaryReaders.append(rd) elif flag: primaryReaders.append(rd) if len(secondaryReaders) + len(primaryReaders) == 0: print('Error: No matching format for file '+imagefile) raise Exception('No image read') errorReport = '' rdbuffer = {} # create temporary storage for file reader for rd in primaryReaders+secondaryReaders: rd.ReInitialize() # purge anything from a previous read rd.errors = "" # clear out any old errors if not rd.ContentsValidator(imagefile): # rejected on cursory check errorReport += "\n "+rd.formatName + ' validator error' if rd.errors: errorReport += ': '+rd.errors continue ParentFrame = G2frame block = 0 repeat = True CreatedIMGitems = [] while repeat: # loop if the reader asks for another pass on the file block += 1 repeat = False if GSASIIpath.GetConfigValue('debug'): flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer) else: flag = False try: flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer) except rd.ImportException as detail: rd.errors += "\n Read exception: "+str(detail) except Exception as detail: import traceback rd.errors += "\n Unhandled read exception: "+str(detail) rd.errors += "\n Traceback info:\n"+str(traceback.format_exc()) if flag: # this read succeeded if rd.Image is None: raise Exception('No image read. Strange!') if GSASIIpath.GetConfigValue('Transpose'): print ('Transposing Image!') rd.Image = rd.Image.T rd.Data['ImageTag'] = rd.repeatcount rd.readfilename = imagefile # Load generic metadata, as configured G2fil.GetColumnMetadata(rd) LoadImage2Tree(imagefile,G2frame,rd.Comments,rd.Data,rd.Npix,rd.Image) repeat = rd.repeat CreatedIMGitems.append(G2frame.Image) if CreatedIMGitems: return CreatedIMGitems else: print('Error reading file '+imagefile) print('Error messages(s)\n'+errorReport) return []
#raise Exception('No image read') def SaveMultipleImg(G2frame): if not G2frame.GPXtree.GetCount(): print ('no images!') return choices = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',]) if len(choices) == 1: names = choices else: dlg = G2G.G2MultiChoiceDialog(G2frame,'Stress/Strain fitting','Select images to fit:',choices) dlg.SetSelections([]) names = [] if dlg.ShowModal() == wx.ID_OK: names = [choices[sel] for sel in dlg.GetSelections()] dlg.Destroy() if not names: return for name in names: Id = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, name) Npix,imagefile,imagetag = G2frame.GPXtree.GetImageLoc(Id) imroot = os.path.splitext(imagefile)[0] if imagetag: imroot += '_' + str(imagetag) Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Image Controls')) print('Writing '+imroot+'.imctrl') File = open(imroot+'.imctrl','w') keys = ['type','wavelength','calibrant','distance','center', 'tilt','rotation','azmthOff','fullIntegrate','LRazimuth', 'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth', 'calibskip','pixLimit','cutoff','calibdmin','chisq','Flat Bkg', 'binType','SampleShape','PolaVal','SampleAbs','dark image','background image'] for key in keys: if key not in Data: continue #uncalibrated! File.write(key+':'+str(Data[key])+'\n') File.close() mask = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Masks')) G2imG.CleanupMasks(mask) print('Writing '+imroot+'.immask') File = open(imroot+'.immask','w') for key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']: File.write(key+':'+str(mask[key])+'\n') File.close()
[docs]def PutG2Image(filename,Comments,Data,Npix,image): 'Write an image as a python pickle - might be better as an .edf file?' File = open(filename,'wb') cPickle.dump([Comments,Data,Npix,image],File,2) File.close() return
objectScanIgnore = [int,bool,float,str,np.float64,np.float32,np.int32,np.int64,np.ndarray,G2obj.G2VarObj,G2obj.ExpressionObj] try: objectScanIgnore += [ma.MaskedArray] # fails in doc builds except AttributeError: pass if '2' in platform.python_version_tuple()[0]: objectScanIgnore += [unicode,long,]
[docs]def objectScan(data,tag,indexStack=[]): '''Recursively scan an object looking for unexpected data types. This is used in debug mode to scan .gpx files for objects we did not intend to be there. ''' if type(data) is list or type(data) is tuple: for i in range(len(data)): val = objectScan(data[i],tag,indexStack+[i]) if val: data[i] = val print('...fixed') elif type(data) is dict: for key in data: val = objectScan(data[key],tag,indexStack+[key]) if val: data[key] = val print('...fixed') elif data is None: return None elif type(data) in objectScanIgnore: return None else: s = 'unexpected object in '+tag for i in indexStack: s += "[{}]".format(i) #print(s,data.__class__.__name__) # loses full name of class print(s,type(data)) global unexpectedObject unexpectedObject = True # fix bad objects if "gdi.Colour" in str(type(data)): return tuple(data) return
def cPickleLoad(fp): if '2' in platform.python_version_tuple()[0]: return cPickle.load(fp) else: return cPickle.load(fp,encoding='latin-1')
[docs]def ProjFileOpen(G2frame,showProvenance=True): 'Read a GSAS-II project file and load into the G2 data tree' if not os.path.exists(G2frame.GSASprojectfile): print ('\n*** Error attempt to open project file that does not exist:\n '+ str(G2frame.GSASprojectfile)) return LastSavedUsing = None filep = open(G2frame.GSASprojectfile,'rb') if showProvenance: print ('loading from file: '+G2frame.GSASprojectfile) GPXphase = os.path.splitext(G2frame.GSASprojectfile)[0]+'.seqPhase' GPXhist = os.path.splitext(G2frame.GSASprojectfile)[0]+'.seqHist' deleteSeq = False hist = None tmpHistIndex = {} updateFromSeq = False if os.path.exists(GPXphase) and os.path.exists(GPXhist): dlg = wx.MessageDialog(G2frame, 'Load results from crashed sequential fit?\nNo deletes the files!', 'Recover partial sequential fit?', wx.YES | wx.NO | wx.CANCEL) dlg.CenterOnParent() try: result = dlg.ShowModal() deleteSeq = result != wx.ID_CANCEL if result == wx.ID_YES: updateFromSeq = True fp = open(GPXphase,'rb') data = cPickleLoad(fp) # first block in file should be Phases if data[0][0] != 'Phases': raise Exception('Unexpected block in {} file. How did this happen?' .format(GPXphase)) Phases = {} for name,vals in data[1:]: Phases[name] = vals name,CovData = cPickleLoad(fp)[0] # 2nd block in file should be Covariance name,RigidBodies = cPickleLoad(fp)[0] # 3rd block in file should be Rigid Bodies fp.close() # index the histogram updates hist = open(GPXhist,'rb') try: while True: loc = hist.tell() datum = cPickleLoad(hist)[0] tmpHistIndex[datum[0]] = loc except EOFError: pass finally: dlg.Destroy() wx.BeginBusyCursor() try: if GSASIIpath.GetConfigValue('show_gpxSize'): posPrev = 0 sizeList = {} while True: try: data = cPickleLoad(filep) except EOFError: break datum = data[0] if GSASIIpath.GetConfigValue('show_gpxSize'): sizeList[datum[0]] = filep.tell()-posPrev posPrev = filep.tell() # scan the GPX file for unexpected objects if GSASIIpath.GetConfigValue('debug'): global unexpectedObject unexpectedObject = False objectScan(data,'tree item "{}" entry '.format(datum[0])) #if unexpectedObject: # print(datum[0]) # GSASIIpath.IPyBreak() Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=datum[0]) if datum[0] == 'Phases' and GSASIIpath.GetConfigValue('SeparateHistPhaseTreeItem',False): G2frame.GPXtree.AppendItem(parent=G2frame.root,text='Hist/Phase') if updateFromSeq and datum[0] == 'Phases': for pdata in data[1:]: if pdata[0] in Phases: pdata[1].update(Phases[pdata[0]]) elif updateFromSeq and datum[0] == 'Covariance': data[0][1] = CovData elif updateFromSeq and datum[0] == 'Rigid bodies': data[0][1] = RigidBodies elif updateFromSeq and datum[0] in tmpHistIndex: hist.seek(tmpHistIndex[datum[0]]) hdata = cPickleLoad(hist) if data[0][0] != hdata[0][0]: print('Error! Updating {} with {}'.format(data[0][0],hdata[0][0])) datum = hdata[0] xferItems = ['Background','Instrument Parameters','Sample Parameters','Reflection Lists'] hItems = {name:j+1 for j,(name,val) in enumerate(hdata[1:]) if name in xferItems} for j,(name,val) in enumerate(data[1:]): if name not in xferItems: continue data[j+1][1] = hdata[hItems[name]][1] if datum[0].startswith('PWDR'): if 'ranId' not in datum[1][0]: # patch: add random Id if not present datum[1][0]['ranId'] = ran.randint(0,sys.maxsize) G2frame.GPXtree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?) elif datum[0].startswith('HKLF'): if 'ranId' not in datum[1][0]: # patch: add random Id if not present datum[1][0]['ranId'] = ran.randint(0,sys.maxsize) G2frame.GPXtree.SetItemPyData(Id,datum[1]) else: G2frame.GPXtree.SetItemPyData(Id,datum[1]) if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]: LastSavedUsing = datum[1]['LastSavedUsing'] if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug') and showProvenance: print('DBG_Packages used to create .GPX file:') if 'dict' in str(type(datum[1]['PythonVersions'])): #patch for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()): print(" {:<14s}: {:s}".format(p[0],p[1])) else: for p in datum[1]['PythonVersions']: print(" {:<12s} {:s}".format(p[0]+':',p[1])) oldPDF = False for datus in data[1:]: #patch - 1/23/17 PDF cleanup if datus[0][:4] in ['I(Q)','S(Q)','F(Q)','G(R)']: oldPDF = True data[1][1][datus[0][:4]] = copy.deepcopy(datus[1][:2]) continue #end PDF cleanup sub = G2frame.GPXtree.AppendItem(Id,datus[0]) #patch if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1: if datum[0].startswith('PWDR'): datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}] else: datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}] for item in datus[1][0]: #zip makes tuples - now make lists! datus[1][0][item] = list(datus[1][0][item]) #end patch G2frame.GPXtree.SetItemPyData(sub,datus[1]) if 'PDF ' in datum[0][:4] and oldPDF: sub = G2frame.GPXtree.AppendItem(Id,'PDF Peaks') G2frame.GPXtree.SetItemPyData(sub,{'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]}) if datum [0].startswith('IMG'): #retrieve image default flag & data if set Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Image Controls')) if Data['setDefault']: G2frame.imageDefault = Data G2frame.imageDefault['setDefault'] = False if 'formatName' in G2frame.imageDefault: del G2frame.imageDefault['formatName'] if LastSavedUsing: print('GPX load successful. Last saved with GSAS-II revision '+LastSavedUsing) else: print('project load successful') if GSASIIpath.GetConfigValue('show_gpxSize'): print(50*'=') print('File section sizes (Kb)') for item in sizeList: print(' {:20s} {:10.3f}'.format( item[:20],sizeList[item]/1024.)) print(50*'=') G2frame.NewPlot = True except Exception as errmsg: if GSASIIpath.GetConfigValue('debug'): print('\nError reading GPX file:',errmsg) import traceback print (traceback.format_exc()) msg = wx.MessageDialog(G2frame,message="Error reading file "+ str(G2frame.GSASprojectfile)+". This is not a current GSAS-II .gpx file", caption="Load Error",style=wx.ICON_ERROR | wx.OK | wx.STAY_ON_TOP) msg.ShowModal() finally: filep.close() wx.EndBusyCursor() G2frame.Status.SetStatusText('Mouse RB drag/drop to reorder',0) if deleteSeq: if hist: hist.close() try: os.remove(GPXphase) except: print('Warning: unable to delete {}'.format(GPXphase)) try: os.remove(GPXhist) except: print('Warning: unable to delete {}'.format(GPXhist)) G2frame.SetTitleByGPX() if LastSavedUsing: try: G2G.updateNotifier(G2frame,int(LastSavedUsing)) except: pass
[docs]def ProjFileSave(G2frame): 'Save a GSAS-II project file' if not G2frame.GPXtree.IsEmpty(): file = open(G2frame.GSASprojectfile,'wb') print ('save to file: '+G2frame.GSASprojectfile) # stick the file name into the tree and version info into tree so they are saved. # (Controls should always be created at this point) try: Controls = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls')) Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile) Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber()) Controls['PythonVersions'] = G2frame.PackageVersions except: pass wx.BeginBusyCursor() try: item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root) while item: data = [] name = G2frame.GPXtree.GetItemText(item) if name.startswith('Hist/Phase'): # skip over this item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie) continue data.append([name,G2frame.GPXtree.GetItemPyData(item)]) item2, cookie2 = G2frame.GPXtree.GetFirstChild(item) while item2: name = G2frame.GPXtree.GetItemText(item2) data.append([name,G2frame.GPXtree.GetItemPyData(item2)]) item2, cookie2 = G2frame.GPXtree.GetNextChild(item, cookie2) item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie) cPickle.dump(data,file,2) file.close() pth = os.path.split(os.path.abspath(G2frame.GSASprojectfile))[0] if GSASIIpath.GetConfigValue('Save_paths'): G2G.SaveGPXdirectory(pth) G2frame.LastGPXdir = pth finally: wx.EndBusyCursor() print('project save successful')
[docs]def SaveIntegration(G2frame,PickId,data,Overwrite=False): 'Save image integration results as powder pattern(s)' waves = {'Cu':[1.54051,1.54433],'Ti':[2.74841,2.75207],'Cr':[2.28962,2.29351], 'Fe':[1.93597,1.93991],'Co':[1.78892,1.79278],'Mo':[0.70926,0.713543], 'Ag':[0.559363,0.563775]} azms = G2frame.Integrate[1] X = G2frame.Integrate[2][:-1] N = len(X) Id = G2frame.GPXtree.GetItemParent(PickId) name = G2frame.GPXtree.GetItemText(Id) name = name.replace('IMG ',data['type']+' ') Comments = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Comments')) Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls')) Comments.append('Dark image = %s\n'%str(data['dark image'])) Comments.append('Background image = %s\n'%str(data['background image'])) Comments.append('Gain map = %s\n'%str(data['Gain map'])) if 'PWDR' in name: if 'target' in data: names = ['Type','Lam1','Lam2','I(L2)/I(L1)','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth'] codes = [0 for i in range(14)] else: if data.get('IfPink',False): names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','alpha-0','alpha-1','beta-0','beta-1','Azimuth'] codes = [0 for i in range(15)] else: names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth'] codes = [0 for i in range(12)] elif 'SASD' in name: names = ['Type','Lam','Zero','Azimuth'] codes = [0 for i in range(4)] X = 4.*np.pi*npsind(X/2.)/data['wavelength'] #convert to q Xminmax = [X[0],X[-1]] Azms = np.zeros(data['outAzimuths']) dazm = 0. if data['outAzimuths'] > 1: dazm = np.min(np.abs(np.diff(azms)))/2. G2frame.IntgOutList = [] for i,azm in enumerate(azms[:-1]): Aname = name+" Azm= %.2f"%((azm+dazm)%360.) item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root) # if Overwrite delete any duplicate if Overwrite and G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname): print('Replacing '+Aname) item = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname) G2frame.GPXtree.Delete(item) else: nOcc = 0 while item: Name = G2frame.GPXtree.GetItemText(item) if Aname in Name: nOcc += 1 item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie) if nOcc: Aname += '(%d)'%(nOcc) Sample = G2obj.SetDefaultSample() #set as Debye-Scherrer Sample['Gonio. radius'] = data['distance'] Sample['Omega'] = data['GonioAngles'][0] Sample['Chi'] = data['GonioAngles'][1] Sample['Phi'] = data['GonioAngles'][2] Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center polariz = data['PolaVal'][0] for item in Comments: for key in ('Temperature','Pressure','Time','FreePrm1','FreePrm2','FreePrm3','Omega', 'Chi','Phi'): if key.lower() in item.lower(): try: Sample[key] = float(item.split('=')[1]) except: pass if 'label_prm' in item.lower(): for num in ('1','2','3'): if 'label_prm'+num in item.lower(): Controls['FreePrm'+num] = item.split('=')[1].strip() if 'PWDR' in Aname: if 'target' in data: #from lab x-ray 2D imaging data wave1,wave2 = waves[data['target']] parms = ['PXC',wave1,wave2,0.5,0.0,polariz,290.,-40.,30.,6.,-14.,0.0,0.0001,Azms[i]] else: if data.get('IfPink',False): parms = ['PXB',data['wavelength'],0.0,polariz,0.,8000.,-150.,-24.,0.,0.,0.,13.,-1300.,3.,-7.,Azms[i]] #from Sect 35 LSS else: parms = ['PXC',data['wavelength'],0.0,polariz,1.0,-0.10,0.4,0.30,1.0,0.0,0.0001,Azms[i]] elif 'SASD' in Aname: Sample['Trans'] = data['SampleAbs'][0] parms = ['LXC',data['wavelength'],0.0,Azms[i]] Y = G2frame.Integrate[0][i] Ymin = np.min(Y) Ymax = np.max(Y) W = np.where(Y>0.,1./Y,1.e-6) #probably not true Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=Aname) G2frame.IntgOutList.append(Id) G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments) G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Limits'),copy.deepcopy([tuple(Xminmax),Xminmax])) if 'PWDR' in Aname: G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Background'),[['chebyschev-1',1,3,1.0,0.0,0.0], {'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[],'background PWDR':['',1.0,False]}]) inst = [dict(zip(names,zip(parms,parms,codes))),{}] for item in inst[0]: inst[0][item] = list(inst[0][item]) G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Instrument Parameters'),inst) if 'PWDR' in Aname: G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample) G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]}) G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Index Peak List'),[[],[]]) G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Unit Cells List'),[]) G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Reflection Lists'),{}) elif 'SASD' in Aname: G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances()) G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample) G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel()) valuesdict = { 'wtFactor':1.0,'Dummy':False,'ranId':ran.randint(0,sys.maxsize),'Offset':[0.0,0.0],'delOffset':0.02*Ymax, 'refOffset':-0.1*Ymax,'refDelt':0.1*Ymax,'Yminmax':[Ymin,Ymax]} G2frame.GPXtree.SetItemPyData(Id,[valuesdict, [np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]]) return Id #last powder pattern generated
[docs]def XYsave(G2frame,XY,labelX='X',labelY='Y',names=[]): 'Save XY table data' pth = G2G.GetExportPath(G2frame) dlg = wx.FileDialog( G2frame, 'Enter csv filename for XY table', pth, '', 'XY table file (*.csv)|*.csv',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT) try: if dlg.ShowModal() == wx.ID_OK: filename = dlg.GetPath() filename = os.path.splitext(filename)[0]+'.csv' File = open(filename,'w') else: filename = None finally: dlg.Destroy() if not filename: return for i in range(len(XY)): if len(names): header = '%s,%s(%s)\n'%(labelX,labelY,names[i]) else: header = '%s,%s(%d)\n'%(labelX,labelY,i) File.write(header) for x,y in XY[i].T: File.write('%.3f,%.3f\n'%(x,y)) File.close() print (' XY data saved to: '+filename)
[docs]def PeakListSave(G2frame,file,peaks): 'Save powder peaks to a data file' print ('save peak list to file: '+G2frame.peaklistfile) if not peaks: dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK) try: dlg.ShowModal() finally: dlg.Destroy() return for peak in peaks: file.write("%10.4f %12.2f %10.3f %10.3f \n" % \ (peak[0],peak[2],peak[4],peak[6])) print ('peak list saved')
[docs]def IndexPeakListSave(G2frame,peaks): 'Save powder peaks from the indexing list' file = open(G2frame.peaklistfile,'wa') print ('save index peak list to file: '+G2frame.peaklistfile) wx.BeginBusyCursor() try: if not peaks: dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK) try: dlg.ShowModal() finally: dlg.Destroy() return for peak in peaks: file.write("%12.6f\n" % (peak[7])) file.close() finally: wx.EndBusyCursor() print ('index peak list saved')
[docs]def ExtractFileFromZip(filename, selection=None, confirmread=True, confirmoverwrite=True, parent=None, multipleselect=False): '''If the filename is a zip file, extract a file from that archive. :param list Selection: used to predefine the name of the file to be extracted. Filename case and zip directory name are ignored in selection; the first matching file is used. :param bool confirmread: if True asks the user to confirm before expanding the only file in a zip :param bool confirmoverwrite: if True asks the user to confirm before overwriting if the extracted file already exists :param bool multipleselect: if True allows more than one zip file to be extracted, a list of file(s) is returned. If only one file is present, do not ask which one, otherwise offer a list of choices (unless selection is used). :returns: the name of the file that has been created or a list of files (see multipleselect) If the file is not a zipfile, return the name of the input file. If the zipfile is empty or no file has been selected, return None ''' import zipfile # do this now, since we can save startup time by doing this only on need import shutil zloc = os.path.split(filename)[0] if not zipfile.is_zipfile(filename): #print("not zip") return filename z = zipfile.ZipFile(filename,'r') zinfo = z.infolist() if len(zinfo) == 0: #print('Zip has no files!') zlist = [-1] if selection: choices = [os.path.split(i.filename)[1].lower() for i in zinfo] if selection.lower() in choices: zlist = [choices.index(selection.lower())] else: print('debug: file '+str(selection)+' was not found in '+str(filename)) zlist = [-1] elif len(zinfo) == 1 and confirmread: result = wx.ID_NO dlg = wx.MessageDialog( parent, 'Is file '+str(zinfo[0].filename)+ ' what you want to extract from '+ str(os.path.split(filename)[1])+'?', 'Confirm file', wx.YES_NO | wx.ICON_QUESTION) try: result = dlg.ShowModal() finally: dlg.Destroy() if result == wx.ID_NO: zlist = [-1] else: zlist = [0] elif len(zinfo) == 1: zlist = [0] elif multipleselect: # select one or more from a from list choices = [i.filename for i in zinfo] dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename), 'Choose file(s)',choices) if dlg.ShowModal() == wx.ID_OK: zlist = dlg.GetSelections() else: zlist = [] dlg.Destroy() else: # select one from a from list choices = [i.filename for i in zinfo] dlg = wx.SingleChoiceDialog(parent, 'Select file to extract from zip file'+str(filename),'Choose file', choices,) if dlg.ShowModal() == wx.ID_OK: zlist = [dlg.GetSelection()] else: zlist = [-1] dlg.Destroy() outlist = [] for zindex in zlist: if zindex >= 0: efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1]) if os.path.exists(efil) and confirmoverwrite: result = wx.ID_NO dlg = wx.MessageDialog(parent, 'File '+str(efil)+' already exists. OK to overwrite it?', 'Confirm overwrite',wx.YES_NO | wx.ICON_QUESTION) try: result = dlg.ShowModal() finally: dlg.Destroy() if result == wx.ID_NO: zindex = -1 if zindex >= 0: # extract the file to the current directory, regardless of it's original path #z.extract(zinfo[zindex],zloc) eloc,efil = os.path.split(zinfo[zindex].filename) outfile = os.path.join(zloc, efil) fpin = z.open(zinfo[zindex]) fpout = open(outfile, "wb") shutil.copyfileobj(fpin, fpout) fpin.close() fpout.close() outlist.append(outfile) z.close() if multipleselect and len(outlist) >= 1: return outlist elif len(outlist) == 1: return outlist[0] else: return None
[docs]def striphist(var,insChar=''): 'strip a histogram number from a var name' sv = var.split(':') if len(sv) <= 1: return var if sv[1]: sv[1] = insChar return ':'.join(sv)
###################################################################### # base classes for reading various types of data files # not used directly, only by subclassing ######################################################################
[docs]class ExportBaseclass(object): '''Defines a base class for the exporting of GSAS-II results. This class is subclassed in the various exports/G2export_*.py files. Those files are imported in :meth:`GSASIIdataGUI.GSASII._init_Exports` which defines the appropriate menu items for each one and the .Exporter method is called directly from the menu item. Routines may also define a .Writer method, which is used to write a single file without invoking any GUI objects. ''' # TODO: review exporters producing exceptions where .Writer can't be used where G2frame is None (see CIF) # TODO: review conflicting uses of .Writer with mode (SeqRef) & elsewhere # TODO: move this class to G2fil def __init__(self,G2frame,formatName,extension,longFormatName=None,): self.G2frame = G2frame self.formatName = formatName # short string naming file type self.extension = extension if longFormatName: # longer string naming file type self.longFormatName = longFormatName else: self.longFormatName = formatName self.OverallParms = {} self.Phases = {} self.Histograms = {} self.powderDict = {} self.sasdDict = {} self.refdDict = {} self.xtalDict = {} self.parmDict = {} self.sigDict = {} self.fp = None # updated in InitExport: self.currentExportType = None # type of export that has been requested # updated in ExportSelect (when used): self.phasenam = None # a list of selected phases self.histnam = None # a list of selected histograms self.filename = None # name of file to be written (single export) or template (multiple files) self.dirname = '' # name of directory where file(s) will be written self.fullpath = '' # name of file being written -- full path # items that should be defined in a subclass of this class self.exporttype = [] # defines the type(s) of exports that the class can handle. # The following types are defined: 'project', "phase", "powder", "single" self.multiple = False # set as True if the class can export multiple phases or histograms # self.multiple is ignored for "project" exports
[docs] def InitExport(self,event): '''Determines the type of menu that called the Exporter and misc initialization. ''' self.filename = None # name of file to be written (single export) self.dirname = '' # name of file to be written (multiple export) if event: self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
[docs] def MakePWDRfilename(self,hist): '''Make a filename root (no extension) from a PWDR histogram name :param str hist: the histogram name in data tree (starts with "PWDR ") ''' file0 = '' file1 = hist[5:] # replace repeated blanks while file1 != file0: file0 = file1 file1 = file0.replace(' ',' ').strip() file0 = file1.replace('Azm= ','A') # if angle has unneeded decimal places on aziumuth, remove them if file0[-3:] == '.00': file0 = file0[:-3] file0 = file0.replace('.','_') file0 = file0.replace(' ','_') return file0
[docs] def ExportSelect(self,AskFile='ask'): '''Selects histograms or phases when needed. Sets a default file name when requested into self.filename; always sets a default directory in self.dirname. :param bool AskFile: Determines how this routine processes getting a location to store the current export(s). * if AskFile is 'ask' (default option), get the name of the file to be written; self.filename and self.dirname are always set. In the case where multiple files must be generated, the export routine should do this based on self.filename as a template. * if AskFile is 'dir', get the name of the directory to be used; self.filename is not used, but self.dirname is always set. The export routine will always generate the file name. * if AskFile is 'single', get only the name of the directory to be used when multiple items will be written (as multiple files) are used *or* a complete file name is requested when a single file name is selected. self.dirname is always set and self.filename used only when a single file is selected. * if AskFile is 'default', creates a name of the file to be used from the name of the project (.gpx) file. If the project has not been saved, then the name of file is requested. self.filename and self.dirname are always set. In the case where multiple file names must be generated, the export routine should do this based on self.filename. * if AskFile is 'default-dir', sets self.dirname from the project (.gpx) file. If the project has not been saved, then a directory is requested. self.filename is not used. :returns: True in case of an error ''' numselected = 1 if self.currentExportType == 'phase': if len(self.Phases) == 0: self.G2frame.ErrorDialog( 'Empty project', 'Project does not contain any phases.') return True elif len(self.Phases) == 1: self.phasenam = list(self.Phases.keys()) elif self.multiple: choices = sorted(self.Phases.keys()) phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True) if phasenum is None: return True self.phasenam = [choices[i] for i in phasenum] if not self.phasenam: return True numselected = len(self.phasenam) else: choices = sorted(self.Phases.keys()) phasenum = G2G.ItemSelector(choices,self.G2frame) if phasenum is None: return True self.phasenam = [choices[phasenum]] numselected = len(self.phasenam) elif self.currentExportType == 'single': if len(self.xtalDict) == 0: self.G2frame.ErrorDialog( 'Empty project', 'Project does not contain any single crystal data.') return True elif len(self.xtalDict) == 1: self.histnam = self.xtalDict.values() elif self.multiple: choices = sorted(self.xtalDict.values()) hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True) if not hnum: return True self.histnam = [choices[i] for i in hnum] numselected = len(self.histnam) else: choices = sorted(self.xtalDict.values()) hnum = G2G.ItemSelector(choices,self.G2frame) if hnum is None: return True self.histnam = [choices[hnum]] numselected = len(self.histnam) elif self.currentExportType == 'powder': if len(self.powderDict) == 0: self.G2frame.ErrorDialog( 'Empty project', 'Project does not contain any powder data.') return True elif len(self.powderDict) == 1: self.histnam = list(self.powderDict.values()) elif self.multiple: choices = sorted(self.powderDict.values()) hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True) if not hnum: return True self.histnam = [choices[i] for i in hnum] numselected = len(self.histnam) else: choices = sorted(self.powderDict.values()) hnum = G2G.ItemSelector(choices,self.G2frame) if hnum is None: return True self.histnam = [choices[hnum]] numselected = len(self.histnam) elif self.currentExportType == 'sasd': if len(self.sasdDict) == 0: self.G2frame.ErrorDialog( 'Empty project', 'Project does not contain any small angle data.') return True elif len(self.sasdDict) == 1: self.histnam = self.sasdDict.values() elif self.multiple: choices = sorted(self.sasdDict.values()) hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True) if not hnum: return True self.histnam = [choices[i] for i in hnum] numselected = len(self.histnam) else: choices = sorted(self.sasdDict.values()) hnum = G2G.ItemSelector(choices,self.G2frame) if hnum is None: return True self.histnam = [choices[hnum]] numselected = len(self.histnam) elif self.currentExportType == 'refd': if len(self.refdDict) == 0: self.G2frame.ErrorDialog( 'Empty project', 'Project does not contain any reflectivity data.') return True elif len(self.refdDict) == 1: self.histnam = self.refdDict.values() elif self.multiple: choices = sorted(self.refdDict.values()) hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True) if not hnum: return True self.histnam = [choices[i] for i in hnum] numselected = len(self.histnam) else: choices = sorted(self.refdDict.values()) hnum = G2G.ItemSelector(choices,self.G2frame) if hnum is None: return True self.histnam = [choices[hnum]] numselected = len(self.histnam) elif self.currentExportType == 'image': if len(self.Histograms) == 0: self.G2frame.ErrorDialog( 'Empty project', 'Project does not contain any images.') return True elif len(self.Histograms) == 1: self.histnam = list(self.Histograms.keys()) else: choices = sorted(self.Histograms.keys()) hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple) if self.multiple: if not hnum: return True self.histnam = [choices[i] for i in hnum] else: if hnum is None: return True self.histnam = [choices[hnum]] numselected = len(self.histnam) if self.currentExportType == 'map': # search for phases with maps mapPhases = [] choices = [] for phasenam in sorted(self.Phases): phasedict = self.Phases[phasenam] # pointer to current phase info if len(phasedict['General']['Map'].get('rho',[])): mapPhases.append(phasenam) if phasedict['General']['Map'].get('Flip'): choices.append('Charge flip map: '+str(phasenam)) elif phasedict['General']['Map'].get('MapType'): choices.append( str(phasedict['General']['Map'].get('MapType')) + ' map: ' + str(phasenam)) else: choices.append('unknown map: '+str(phasenam)) # select a map if needed if len(mapPhases) == 0: self.G2frame.ErrorDialog( 'Empty project', 'Project does not contain any maps.') return True elif len(mapPhases) == 1: self.phasenam = mapPhases else: phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple) if self.multiple: if not phasenum: return True self.phasenam = [mapPhases[i] for i in phasenum] else: if phasenum is None: return True self.phasenam = [mapPhases[phasenum]] numselected = len(self.phasenam) # items selected, now set self.dirname and usually self.filename if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or ( AskFile == 'default' and not self.G2frame.GSASprojectfile ): filename = self.askSaveFile() if not filename: return True self.dirname,self.filename = os.path.split(filename) elif AskFile == 'dir' or AskFile == 'single' or ( AskFile == 'default-dir' and not self.G2frame.GSASprojectfile ): self.dirname = self.askSaveDirectory() if not self.dirname: return True elif AskFile == 'default-dir' or AskFile == 'default': self.dirname,self.filename = os.path.split( os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension ) else: raise Exception('This should not happen!')
[docs] def loadParmDict(self): '''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update refined values to those from the last cycle and set the uncertainties for the refined parameters in another dict (self.sigDict). Expands the parm & sig dicts to include values derived from constraints. This could be made faster for sequential fits by reducing the histogram list to only the active histogram being exported. ''' self.G2frame.CheckNotebook() self.parmDict = {} self.sigDict = {} rigidbodyDict = {} covDict = {} consDict = {} Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree() if self.G2frame.GPXtree.IsEmpty(): return # nothing to do item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root) while item: name = self.G2frame.GPXtree.GetItemText(item) if name == 'Rigid bodies': rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(item) elif name == 'Covariance': covDict = self.G2frame.GPXtree.GetItemPyData(item) elif name == 'Constraints': consDict = self.G2frame.GPXtree.GetItemPyData(item) item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie) rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False) self.parmDict.update(rbDict) rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]}) Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData( Phases,RestraintDict=None,rbIds=rbIds,Print=False) self.parmDict.update(phaseDict) hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData( Phases,Histograms,Print=False,resetRefList=False) self.parmDict.update(hapDict) histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False) self.parmDict.update(histDict) self.parmDict.update(zip( covDict.get('varyList',[]), covDict.get('variables',[]))) self.sigDict = dict(zip( covDict.get('varyList',[]), covDict.get('sig',[]))) # expand to include constraints: first compile a list of constraints constList = [] for item in consDict: if item.startswith('_'): continue constList += consDict[item] # now process the constraints G2mv.InitVars() constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList) varyList = covDict.get('varyListStart') if varyList is None and len(constDict) == 0: # no constraints can use varyList varyList = covDict.get('varyList') elif varyList is None: # old GPX file from before pre-constraint varyList is saved print (' *** Old refinement: Please use Calculate/Refine to redo ***') raise Exception(' *** Export aborted ***') else: varyList = list(varyList) # add symmetry-generated constraints rigidbodyDict = self.G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Rigid bodies')) rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]}) rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False) Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData( Phases,RestraintDict=None,rbIds=rbIds,Print=False) # generates atom symmetry constraints msg = G2mv.EvaluateMultipliers(constDict,phaseDict) if msg: print('Unable to interpret multiplier(s): '+msg) raise Exception(' *** CIF creation aborted ***') try: G2mv.GenerateConstraints(varyList,constDict,fixedList,self.parmDict) #print(G2mv.VarRemapShow(varyList)) except: # this really should not happen print (' *** ERROR - constraints are internally inconsistent ***') errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList) print ('Errors'+errmsg) if warnmsg: print ('Warnings'+warnmsg) raise Exception(' *** CIF creation aborted ***') # add the constrained values to the parameter dictionary G2mv.Dict2Map(self.parmDict,varyList) # and add their uncertainties into the esd dictionary (sigDict) if covDict.get('covMatrix') is not None: self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
[docs] def loadTree(self): '''Load the contents of the data tree into a set of dicts (self.OverallParms, self.Phases and self.Histogram as well as self.powderDict & self.xtalDict) * The childrenless data tree items are overall parameters/controls for the entire project and are placed in self.OverallParms * Phase items are placed in self.Phases * Data items are placed in self.Histogram. The key for these data items begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type. ''' self.OverallParms = {} self.powderDict = {} self.sasdDict = {} self.refdDict = {} self.xtalDict = {} self.Phases = {} self.Histograms = {} self.SeqRefdata = None self.SeqRefhist = None if self.G2frame.GPXtree.IsEmpty(): return # nothing to do histType = None if self.currentExportType == 'phase': # if exporting phases load them here sub = G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Phases') if not sub: print ('no phases found') return True item, cookie = self.G2frame.GPXtree.GetFirstChild(sub) while item: phaseName = self.G2frame.GPXtree.GetItemText(item) self.Phases[phaseName] = self.G2frame.GPXtree.GetItemPyData(item) item, cookie = self.G2frame.GPXtree.GetNextChild(sub, cookie) # Get rigid body info into self.OverallParms for key in ('Rigid bodies','Covariance'): item = G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,key) if item: self.OverallParms[key] = self.G2frame.GPXtree.GetItemPyData(item) item, cookie = self.G2frame.GPXtree.GetNextChild(sub, cookie) return elif self.currentExportType == 'single': histType = 'HKLF' elif self.currentExportType == 'powder': histType = 'PWDR' elif self.currentExportType == 'image': histType = 'IMG' elif self.currentExportType == 'sasd': histType = 'SASD' elif self.currentExportType == 'refd': histType = 'REFD' if histType: # Loading just one kind of tree entry item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root) while item: name = self.G2frame.GPXtree.GetItemText(item) if name.startswith(histType): if self.Histograms.get(name): # there is already an item with this name print('Histogram name '+str(name)+' is repeated. Renaming') if name[-1] == '9': name = name[:-1] + '10' elif name[-1] in '012345678': name = name[:-1] + str(int(name[-1])+1) else: name += '-1' self.Histograms[name] = {} # the main info goes into Data, but the 0th # element contains refinement results, carry # that over too now. self.Histograms[name]['Data'] = self.G2frame.GPXtree.GetItemPyData(item)[1] self.Histograms[name][0] = self.G2frame.GPXtree.GetItemPyData(item)[0] item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item) while item2: child = self.G2frame.GPXtree.GetItemText(item2) self.Histograms[name][child] = self.G2frame.GPXtree.GetItemPyData(item2) item2, cookie2 = self.G2frame.GPXtree.GetNextChild(item, cookie2) item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie) # index powder and single crystal histograms by number for hist in self.Histograms: if hist.startswith("PWDR"): d = self.powderDict elif hist.startswith("HKLF"): d = self.xtalDict elif hist.startswith("SASD"): d = self.sasdDict elif hist.startswith("REFD"): d = self.refdDict else: return i = self.Histograms[hist].get('hId') if i is None and not d.keys(): i = 0 elif i is None or i in d.keys(): i = max(d.keys())+1 d[i] = hist return # else standard load: using all interlinked phases and histograms self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree() item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root) while item: name = self.G2frame.GPXtree.GetItemText(item) item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item) if not item2: self.OverallParms[name] = self.G2frame.GPXtree.GetItemPyData(item) item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie) # index powder and single crystal histograms for hist in self.Histograms: i = self.Histograms[hist]['hId'] if hist.startswith("PWDR"): self.powderDict[i] = hist elif hist.startswith("HKLF"): self.xtalDict[i] = hist elif hist.startswith("SASD"): self.sasdDict[i] = hist elif hist.startswith("REFD"): self.refdDict[i] = hist
[docs] def dumpTree(self,mode='type'): '''Print out information on the data tree dicts loaded in loadTree. Used for testing only. ''' if self.SeqRefdata and self.SeqRefhist: print('Note that dumpTree does not show sequential results') print ('\nOverall') if mode == 'type': def Show(arg): return type(arg) else: def Show(arg): return arg for key in self.OverallParms: print (' '+key+Show(self.OverallParms[key])) print ('Phases') for key1 in self.Phases: print (' '+key1+Show(self.Phases[key1])) print ('Histogram') for key1 in self.Histograms: print (' '+key1+Show(self.Histograms[key1])) for key2 in self.Histograms[key1]: print (' '+key2+Show(self.Histograms[key1][key2]))
def defaultSaveFile(self): return os.path.abspath( os.path.splitext(self.G2frame.GSASprojectfile )[0]+self.extension)
[docs] def askSaveFile(self): '''Ask the user to supply a file name :returns: a file name (str) or None if Cancel is pressed ''' #pth = G2G.GetExportPath(self.G2frame) if self.G2frame.GSASprojectfile: defnam = os.path.splitext( os.path.split(self.G2frame.GSASprojectfile)[1] )[0]+self.extension else: defnam = 'default' + self.extension return G2G.askSaveFile(self.G2frame,defnam,self.extension,self.longFormatName)
[docs] def askSaveDirectory(self): '''Ask the user to supply a directory name. Path name is used as the starting point for the next export path search. :returns: a directory name (str) or None if Cancel is pressed TODO: Can this be replaced with G2G.askSaveDirectory? ''' pth = G2G.GetExportPath(self.G2frame) dlg = wx.DirDialog( self.G2frame, 'Input directory where file(s) will be written', pth, wx.DD_DEFAULT_STYLE) dlg.CenterOnParent() try: if dlg.ShowModal() == wx.ID_OK: filename = dlg.GetPath() self.G2frame.LastExportDir = filename else: filename = None finally: dlg.Destroy() return filename
# Tools for file writing.
[docs] def OpenFile(self,fil=None,mode='w'): '''Open the output file :param str fil: The name of the file to open. If None (default) the name defaults to self.dirname + self.filename. If an extension is supplied, it is not overridded, but if not, the default extension is used. :returns: the file object opened by the routine which is also saved as self.fp ''' if mode == 'd': # debug mode self.fullpath = '(stdout)' self.fp = sys.stdout return if not fil: if not os.path.splitext(self.filename)[1]: self.filename += self.extension fil = os.path.join(self.dirname,self.filename) self.fullpath = os.path.abspath(fil) self.fp = open(self.fullpath,mode) return self.fp
[docs] def Write(self,line): '''write a line of output, attaching a line-end character :param str line: the text to be written. ''' if self.fp is None: raise Exception('Attempt to Write without use of OpenFile') self.fp.write(line+'\n')
[docs] def CloseFile(self,fp=None): '''Close a file opened in OpenFile :param file fp: the file object to be closed. If None (default) file object self.fp is closed. ''' if self.fp is None: raise Exception('Attempt to CloseFile without use of OpenFile') if self.fp == sys.stdout: return # debug mode if fp is None: fp = self.fp self.fp = None if fp is not None: fp.close()
[docs] def SetSeqRef(self,data,hist): '''Set the exporter to retrieve results from a sequential refinement rather than the main tree ''' self.SeqRefdata = data self.SeqRefhist = hist data_name = data[hist] for i,val in zip(data_name['varyList'],data_name['sig']): self.sigDict[i] = val self.sigDict[striphist(i)] = val for i in data_name['parmDict']: self.parmDict[striphist(i)] = data_name['parmDict'][i] self.parmDict[i] = data_name['parmDict'][i] # zero out the dA[xyz] terms, they would only bring confusion key = i.split(':') if len(key) < 3: continue if key[2].startswith('dA'): self.parmDict[i] = 0.0 for i,(val,sig) in data_name.get('depParmDict',{}).items(): self.parmDict[i] = val self.sigDict[i] = sig
#GSASIIpath.IPyBreak() # Tools to pull information out of the data arrays
[docs] def GetCell(self,phasenam): """Gets the unit cell parameters and their s.u.'s for a selected phase :param str phasenam: the name for the selected phase :returns: `cellList,cellSig` where each is a 7 element list corresponding to a, b, c, alpha, beta, gamma, volume where `cellList` has the cell values and `cellSig` has their uncertainties. """ if self.SeqRefdata and self.SeqRefhist: return self.GetSeqCell(phasenam,self.SeqRefdata[self.SeqRefhist]) phasedict = self.Phases[phasenam] # pointer to current phase info try: pfx = str(phasedict['pId'])+'::' A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict) cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A, self.OverallParms['Covariance']) # returns 7 vals, includes sigVol cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),) return cellList,cellSig except KeyError: cell = phasedict['General']['Cell'][1:] return cell,7*[0]
[docs] def GetSeqCell(self,phasenam,data_name): """Gets the unit cell parameters and their s.u.'s for a selected phase and histogram in a sequential fit :param str phasenam: the name for the selected phase :param dict data_name: the sequential refinement parameters for the selected histogram :returns: `cellList,cellSig` where each is a 7 element list corresponding to a, b, c, alpha, beta, gamma, volume where `cellList` has the cell values and `cellSig` has their uncertainties. """ phasedict = self.Phases[phasenam] SGdata = phasedict['General']['SGData'] pId = phasedict['pId'] RecpCellTerms = G2lat.cell2A(phasedict['General']['Cell'][1:7]) ESDlookup = {} Dlookup = {} varied = [striphist(i) for i in data_name['varyList']] for item,val in data_name['newCellDict'].items(): if item in varied: ESDlookup[val[0]] = item Dlookup[item] = val[0] A = RecpCellTerms[:] for i in range(6): var = str(pId)+'::A'+str(i) if var in ESDlookup: A[i] = data_name['newCellDict'][ESDlookup[var]][1] # override with refined value cellDict = dict(zip([str(pId)+'::A'+str(i) for i in range(6)],A)) zeroDict = {i:0.0 for i in cellDict} A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata,cellDict,zeroDict) covData = { 'varyList': [Dlookup.get(striphist(v),v) for v in data_name['varyList']], 'covMatrix': data_name['covMatrix'] } return list(G2lat.A2cell(A)) + [G2lat.calc_V(A)], G2stIO.getCellEsd(str(pId)+'::',SGdata,A,covData)
[docs] def GetAtoms(self,phasenam): """Gets the atoms associated with a phase. Can be used with standard or macromolecular phases :param str phasenam: the name for the selected phase :returns: a list of items for eac atom where each item is a list containing: label, typ, mult, xyz, and td, where * label and typ are the atom label and the scattering factor type (str) * mult is the site multiplicity (int) * xyz is contains a list with four pairs of numbers: x, y, z and fractional occupancy and their standard uncertainty (or a negative value) * td is contains a list with either one or six pairs of numbers: if one number it is U\\ :sub:`iso` and with six numbers it is U\\ :sub:`11`, U\\ :sub:`22`, U\\ :sub:`33`, U\\ :sub:`12`, U\\ :sub:`13` & U\\ :sub:`23` paired with their standard uncertainty (or a negative value) """ phasedict = self.Phases[phasenam] # pointer to current phase info cx,ct,cs,cia = phasedict['General']['AtomPtrs'] cfrac = cx+3 fpfx = str(phasedict['pId'])+'::Afrac:' atomslist = [] for i,at in enumerate(phasedict['Atoms']): if phasedict['General']['Type'] == 'macromolecular': label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2]) else: label = at[ct-1] fval = self.parmDict.get(fpfx+str(i),at[cfrac]) fsig = self.sigDict.get(fpfx+str(i),-0.009) mult = at[cs+1] typ = at[ct] xyz = [] for j,v in enumerate(('x','y','z')): val = at[cx+j] pfx = str(phasedict['pId']) + '::A' + v + ':' + str(i) val = self.parmDict.get(pfx, val) dpfx = str(phasedict['pId'])+'::dA'+v+':'+str(i) sig = self.sigDict.get(dpfx,-0.000009) xyz.append((val,sig)) xyz.append((fval,fsig)) td = [] if at[cia] == 'I': pfx = str(phasedict['pId'])+'::AUiso:'+str(i) val = self.parmDict.get(pfx,at[cia+1]) sig = self.sigDict.get(pfx,-0.0009) td.append((val,sig)) else: for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')): pfx = str(phasedict['pId'])+'::'+var+':'+str(i) val = self.parmDict.get(pfx,at[cia+2+i]) sig = self.sigDict.get(pfx,-0.0009) td.append((val,sig)) atomslist.append((label,typ,mult,xyz,td)) return atomslist
######################################################################
[docs]def ExportPowderList(G2frame): '''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder` along with their descriptions (note that a extension may be repeated but descriptions are unique). This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only. :param wx.Frame G2frame: the GSAS-II main data tree window ''' extList = [] extLabel = [] for obj in G2frame.exporterlist: if 'powder' in obj.exporttype: try: obj.Writer extList.append(obj.extension) extLabel.append(obj.formatName) except AttributeError: pass return extList,extLabel
[docs]def ExportPowder(G2frame,TreeName,fileroot,extension,hint=''): '''Writes a single powder histogram using the Export routines. This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only. :param wx.Frame G2frame: the GSAS-II main data tree window :param str TreeName: the name of the histogram (PWDR ...) in the data tree :param str fileroot: name for file to be written, extension ignored :param str extension: extension for file to be written (start with '.'). Must match a powder export routine that has a Writer object. :param str hint: a string that must match the export's format ''' filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension) for obj in G2frame.exporterlist: if obj.extension == extension and 'powder' in obj.exporttype: if hint and hint not in obj.formatName: continue obj.currentExportType = 'powder' obj.InitExport(None) obj.loadTree() # load all histograms in tree into dicts if TreeName not in obj.Histograms: raise Exception('Histogram not found: '+str(TreeName)) try: obj.Writer except AttributeError: continue try: obj.Writer(TreeName,filename) print('wrote file '+filename) return except Exception: print('Export Routine for '+extension+' failed.') else: print('No Export routine supports extension '+extension)
[docs]def ExportSequential(G2frame,data,obj,exporttype): ''' Used to export from every phase/dataset in a sequential refinement using a .Writer method for either projects or phases. Prompts to select histograms and for phase exports, which phase(s). :param wx.Frame G2frame: the GSAS-II main data tree window :param dict data: the sequential refinement data object :param str exporttype: indicates the type of export ('project' or 'phase') ''' if len(data['histNames']) == 0: G2G.G2MessageBox(G2frame,'There are no sequential histograms','Warning') obj.InitExport(None) obj.loadTree() obj.loadParmDict() if len(data['histNames']) == 1: histlist = data['histNames'] else: dlg = G2G.G2MultiChoiceDialog(G2frame,'Select histograms to export from list', 'Select histograms',data['histNames']) if dlg.ShowModal() == wx.ID_OK: histlist = [data['histNames'][l] for l in dlg.GetSelections()] dlg.Destroy() else: dlg.Destroy() return if exporttype == 'Phase': phaselist = list(obj.Phases.keys()) if len(obj.Phases) == 0: G2G.G2MessageBox(G2frame,'There are no phases in sequential ref.','Warning') return elif len(obj.Phases) > 1: dlg = G2G.G2MultiChoiceDialog(G2frame,'Select phases to export from list', 'Select phases', phaselist) if dlg.ShowModal() == wx.ID_OK: phaselist = [phaselist[l] for l in dlg.GetSelections()] dlg.Destroy() else: dlg.Destroy() return filename = obj.askSaveFile() if not filename: return True obj.dirname,obj.filename = os.path.split(filename) print('Writing output to file '+str(obj.filename)+"...") mode = 'w' for p in phaselist: for h in histlist: obj.SetSeqRef(data,h) #GSASIIpath.IPyBreak() obj.Writer(h,phasenam=p,mode=mode) mode = 'a' print('...done') elif exporttype == 'Project': # note that the CIF exporter is not yet ready for this filename = obj.askSaveFile() if not filename: return True obj.dirname,obj.filename = os.path.split(filename) print('Writing output to file '+str(obj.filename)+"...") mode = 'w' for h in histlist: obj.SetSeqRef(data,h) obj.Writer(h,mode=mode) print('\t'+str(h)+' written') mode = 'a' print('...done') elif exporttype == 'Powder': filename = obj.askSaveFile() if not filename: return True obj.dirname,obj.filename = os.path.split(filename) print('Writing output to file '+str(obj.filename)+"...") mode = 'w' for h in histlist: obj.SetSeqRef(data,h) obj.Writer(h,mode=mode) print('\t'+str(h)+' written') mode = 'a' print('...done')
def ReadDIFFaX(DIFFaXfile): print ('read '+DIFFaXfile) Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]], 'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}} df = open(DIFFaXfile,'r') lines = df.readlines() df.close() struct = False Struct = [] stack = False Stack = [] trans = False Trans = [] for diff in lines: diff = diff[:-1].lower() if '!' in diff: continue while '}' in diff: #strip comments iB = diff.index('{') iF = diff.index('}')+1 if iB: diff = diff[:iB] else: diff = diff[iF:] if not diff: continue if diff.strip() == 'instrumental': continue if diff.strip() == 'structural': struct = True continue elif diff.strip() == 'stacking': struct = False stack = True continue elif diff.strip() == 'transitions': stack = False trans = True continue diff = diff.strip() if struct: if diff: Struct.append(diff) elif stack: if diff: Stack.append(diff) elif trans: if diff: Trans.append(diff) #STRUCTURE records laueRec = Struct[1].split() Layer['Laue'] = laueRec[0] if Layer['Laue'] == 'unknown' and len(laueRec) > 1: Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'? if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)' if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)' cell = Struct[0].split() Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0] nLayers = int(Struct[2]) N = 3 if 'layer' not in Struct[3]: N = 4 if Struct[3] != 'infinite': width = Struct[3].split() Layer['Width'][0] = [float(width[0]),float(width[1])] for nL in range(nLayers): if '=' in Struct[N]: name = Struct[N].split('=') sameas = int(name[1])-1 Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]}) N += 1 continue Symm = 'None' if 'centro' in Struct[N+1]: Symm = '-1' Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]}) N += 2 while 'layer' not in Struct[N]: atom = Struct[N][4:].split() atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize()) if atomType not in Layer['AtInfo']: Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType) atomName = '%s(%s)'%(atomType,atom[0]) newVals = [] for val in atom[1:6]: if '/' in val: newVals.append(eval(val+'.')) else: newVals.append(float(val)) atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568] Layer['Layers'][-1]['Atoms'].append(atomRec) N += 1 if N > len(Struct)-1: break #TRANSITIONS records transArray = [] N = 0 for i in range(nLayers): transArray.append([]) for j in range(nLayers): vals = Trans[N].split() newVals = [] for val in vals[:4]: if '/' in val: newVals.append(eval(val+'.')) else: newVals.append(float(val)) transArray[-1].append(newVals+['',False]) N += 1 Layer['Transitions'] = transArray #STACKING records Layer['Stacking'] = [Stack[0],''] if Stack[0] == 'recursive': Layer['Stacking'][1] = Stack[1] elif Stack[0] == 'explicit': if Stack[1] == 'random': Layer['Stacking'][1] = Stack[1] else: Layer['Stacking'][1] = 'list' Layer['Stacking'].append('') for stack in Stack[2:]: Layer['Stacking'][2] += ' '+stack return Layer
[docs]def postURL(URL,postdict): '''Posts a set of values as from a web form. If access fails to an https site the access is retried with http. :param str URL: the URL to post; typically something like 'http://www.../dir/page?' :param dict postdict: contains keywords and values, such as {'centrosymmetry': '0', 'crystalsystem': '0', ...} :returns: a string with the response from the web server or None if access fails. ''' try: import requests # delay this until now, since rarely needed except: # this import seems to fail with the Anaconda pythonw on # macs; it should not! print('Warning: failed to import requests. Python config error') return None repeat = True while repeat: r = None repeat = False try: r = requests.get(URL,params=postdict) if r.status_code == 200: print('request OK') page = r.text return page # success else: print('request to {} failed. Reason={}'.format(URL,r.reason)) except Exception as msg: #ConnectionError? print('connection error - not on internet?') if GSASIIpath.GetConfigValue('debug'): print(msg) finally: if r: r.close() if URL.startswith('https:'): repeat = True URL = URL.replace('https:','http:') else: return None
if __name__ == '__main__': import GSASIIdataGUI application = GSASIIdataGUI.GSASIImain(0) G2frame = application.main #app = wx.PySimpleApp() #G2frame = wx.Frame(None) # create a frame #frm.Show(True) #filename = '/tmp/notzip.zip' #filename = '/tmp/all.zip' #filename = '/tmp/11bmb_7652.zip' #selection=None, confirmoverwrite=True, parent=None #print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm) #print ExtractFileFromZip(filename,multipleselect=True) # #confirmread=False, confirmoverwrite=False) # choicelist=[ ('a','b','c'), # ('test1','test2'),('no choice',)] # titles = [ 'a, b or c', 'tests', 'No option here'] # dlg = MultipleChoicesDialog( # choicelist,titles, # parent=frm) # if dlg.ShowModal() == wx.ID_OK: # print 'Got OK' imagefile = '/tmp/NDC5_00237_3.ge3' Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None) print("\n\nResults loaded to Comments, Data, Npix and Image\n\n") GSASIIpath.IPyBreak_base()