#!/usr/bin/env python # -*- coding: utf-8 -*- #GSASII ########### SVN repository information ################### # $Date: 2013-11-22 22:24:29 +0000 (Fri, 22 Nov 2013) $ # $Author: toby $ # $Revision: 1147 $ # $URL: trunk/GSASII.py $ # $Id: GSASII.py 1147 2013-11-22 22:24:29Z toby $ ########### SVN repository information ################### ''' *GSAS-II Main Module* ===================== Main routines for the GSAS-II program ''' import os import sys import math import copy import random as ran import time import copy import glob import imp import inspect import numpy as np import scipy as sp import wx import matplotlib as mpl try: import OpenGL as ogl except ImportError: print('*******************************************************') print('PyOpenGL is missing from your python installation') print(' - we will try to install it') print('*******************************************************') def install_with_easyinstall(package): try: print "trying a system-wide PyOpenGl install" easy_install.main(['-f',os.path.split(__file__)[0],package]) return except: pass try: print "trying a user level PyOpenGl install" easy_install.main(['-f',os.path.split(__file__)[0],'--user',package]) return except: print "Install of '+package+' failed. Please report this information:" import traceback print traceback.format_exc() sys.exit() from setuptools.command import easy_install install_with_easyinstall('PyOpenGl') print('*******************************************************') print('OpenGL has been installed. Please restart GSAS-II') print('*******************************************************') sys.exit() # load the GSAS routines import GSASIIpath GSASIIpath.SetVersionNumber("$Revision: 1147 $") import GSASIIIO as G2IO import GSASIIgrid as G2gd import GSASIIplot as G2plt import GSASIIpwd as G2pwd import GSASIIpwdGUI as G2pdG import GSASIIspc as G2spc import GSASIIstrMain as G2stMn import GSASIIstrIO as G2stIO import GSASIImapvars as G2mv import GSASIIobj as G2obj #wx inspector - use as needed wxInspector = False # print versions print "Python module versions loaded:" print "python: ",sys.version[:5] print "wxpython: ",wx.__version__ print "matplotlib: ",mpl.__version__ print "numpy: ",np.__version__ print "scipy: ",sp.__version__ print "OpenGL: ",ogl.__version__ try: import mkl print "Max threads ",mkl.get_max_threads() except: pass # print "MKL module not present" __version__ = '0.2.0' G2gd.__version__ = __version__ print "This is GSAS-II version: ",__version__,' revision '+str(GSASIIpath.GetVersionNumber()) # useful degree trig functions sind = lambda x: math.sin(x*math.pi/180.) cosd = lambda x: math.cos(x*math.pi/180.) tand = lambda x: math.tan(x*math.pi/180.) asind = lambda x: 180.*math.asin(x)/math.pi acosd = lambda x: 180.*math.acos(x)/math.pi atan2d = lambda x,y: 180.*math.atan2(y,x)/math.pi def create(parent): return GSASII(parent) class GSASII(wx.Frame): '''Define the main GSAS-II frame and its associated menu items ''' def _Add_FileMenuItems(self, parent): item = parent.Append( help='Open a GSAS-II project file (*.gpx)', id=wx.ID_ANY, kind=wx.ITEM_NORMAL,text='&Open project...') self.Bind(wx.EVT_MENU, self.OnFileOpen, id=item.GetId()) item = parent.Append( help='Save project under current name', id=wx.ID_ANY, kind=wx.ITEM_NORMAL,text='&Save project') self.Bind(wx.EVT_MENU, self.OnFileSave, id=item.GetId()) item = parent.Append( help='Save current project to new file', id=wx.ID_ANY, kind=wx.ITEM_NORMAL,text='Save project as...') self.Bind(wx.EVT_MENU, self.OnFileSaveas, id=item.GetId()) item = parent.Append( help='Create empty new project, saving current is optional', id=wx.ID_ANY, kind=wx.ITEM_NORMAL,text='&New project') self.Bind(wx.EVT_MENU, self.OnFileClose, id=item.GetId()) item = parent.Append( help='Exit from GSAS-II', id=wx.ID_ANY, kind=wx.ITEM_NORMAL,text='&Exit') self.Bind(wx.EVT_MENU, self.OnFileExit, id=item.GetId()) def _Add_DataMenuItems(self,parent): item = parent.Append( help='',id=wx.ID_ANY, kind=wx.ITEM_NORMAL, text='Read image data...') self.Bind(wx.EVT_MENU, self.OnImageRead, id=item.GetId()) item = parent.Append( help='',id=wx.ID_ANY, kind=wx.ITEM_NORMAL, text='Read Powder Pattern Peaks...') self.Bind(wx.EVT_MENU, self.OnReadPowderPeaks, id=item.GetId()) item = parent.Append( help='',id=wx.ID_ANY, kind=wx.ITEM_NORMAL, text='Sum powder data') self.Bind(wx.EVT_MENU, self.OnPwdrSum, id=item.GetId()) item = parent.Append( help='',id=wx.ID_ANY, kind=wx.ITEM_NORMAL, text='Sum image data') self.Bind(wx.EVT_MENU, self.OnImageSum, id=item.GetId()) item = parent.Append( help='',id=wx.ID_ANY, kind=wx.ITEM_NORMAL, text='Add phase') self.Bind(wx.EVT_MENU, self.OnAddPhase, id=item.GetId()) item = parent.Append( help='',id=wx.ID_ANY, kind=wx.ITEM_NORMAL, text='Delete phase') self.Bind(wx.EVT_MENU, self.OnDeletePhase, id=item.GetId()) item = parent.Append( help='',id=wx.ID_ANY, kind=wx.ITEM_NORMAL, text='Rename data') self.Bind(wx.EVT_MENU, self.OnRenameData, id=item.GetId()) item = parent.Append( help='',id=wx.ID_ANY, kind=wx.ITEM_NORMAL, text='Delete data') self.Bind(wx.EVT_MENU, self.OnDataDelete, id=item.GetId()) def _Add_CalculateMenuItems(self,parent): item = parent.Append(help='Make new PDFs from selected powder patterns', id=wx.ID_ANY, kind=wx.ITEM_NORMAL,text='Make new PDFs') self.MakePDF.append(item) # item.Enable(False) self.Bind(wx.EVT_MENU, self.OnMakePDFs, id=item.GetId()) item = parent.Append(help='View least squares parameters', id=wx.ID_ANY, kind=wx.ITEM_NORMAL,text='&View LS parms') self.Bind(wx.EVT_MENU, self.ShowLSParms, id=item.GetId()) item = parent.Append(help='', id=wx.ID_ANY, kind=wx.ITEM_NORMAL, text='&Refine') if len(self.Refine): # extend state for new menus to match main (on mac) state = self.Refine[0].IsEnabled() else: state = False item.Enable(state) self.Refine.append(item) self.Bind(wx.EVT_MENU, self.OnRefine, id=item.GetId()) item = parent.Append(help='', id=wx.ID_ANY, kind=wx.ITEM_NORMAL, text='Sequential refine') if len(self.SeqRefine): # extend state for new menus to match main (on mac) state = self.SeqRefine[0].IsEnabled() else: state = False item.Enable(state) self.SeqRefine.append(item) self.Bind(wx.EVT_MENU, self.OnSeqRefine, id=item.GetId()) def _init_Imports(self): '''import all the G2phase*.py & G2sfact*.py & G2pwd*.py files that are found in the path ''' self.ImportPhaseReaderlist = [] self._init_Import_routines('phase',self.ImportPhaseReaderlist,'Phase') self.ImportSfactReaderlist = [] self._init_Import_routines('sfact',self.ImportSfactReaderlist,'Struct_Factor') self.ImportPowderReaderlist = [] self._init_Import_routines('pwd',self.ImportPowderReaderlist,'Powder_Data') self.ImportMenuId = {} def _init_Import_routines(self,prefix,readerlist,errprefix): '''import all the import readers matching the prefix ''' #path2GSAS2 = os.path.dirname(os.path.realpath(__file__)) # location of this file #pathlist = sys.path[:] #if path2GSAS2 not in pathlist: pathlist.append(path2GSAS2) #path2GSAS2 = os.path.join( # os.path.dirname(os.path.realpath(__file__)), # location of this file # 'imports') pathlist = sys.path[:] #if path2GSAS2 not in pathlist: pathlist.append(path2GSAS2) filelist = [] for path in pathlist: for filename in glob.iglob(os.path.join( path, "G2"+prefix+"*.py")): filelist.append(filename) #print 'debug: found',filename filelist = sorted(list(set(filelist))) # remove duplicates for filename in filelist: path,rootname = os.path.split(filename) pkg = os.path.splitext(rootname)[0] try: fp = None fp, fppath,desc = imp.find_module(pkg,[path,]) pkg = imp.load_module(pkg,fp,fppath,desc) for clss in inspect.getmembers(pkg): # find classes defined in package if clss[0].startswith('_'): continue if inspect.isclass(clss[1]): # check if we have the required methods for m in 'Reader','ExtensionValidator','ContentsValidator': if not hasattr(clss[1],m): break if not callable(getattr(clss[1],m)): break else: reader = clss[1]() # create an import instance readerlist.append(reader) except AttributeError: print 'Import_'+errprefix+': Attribute Error'+str(filename) pass except ImportError: print 'Import_'+errprefix+': Error importing file'+str(filename) pass if fp: fp.close() def OnImportGeneric(self,reader,readerlist,label,multiple=False,usedRanIdList=[]): '''Used to import Phases, powder dataset or single crystal datasets (structure factor tables) using reader objects subclassed from :class:`GSASIIIO.ImportPhase`, :class:`GSASIIIO.ImportStructFactor` or :class:`GSASIIIO.ImportPowderData`. If a reader is specified, only that will be attempted, but if no reader is specified, every one that is potentially compatible (by file extension) will be tried on the selected file(s). :param readerobject reader: This will be a reference to a particular object to be used to read a file or None, if every appropriate reader should be used. :param list readerlist: a list of reader objects appropriate for the current read attempt. At present, this will be either self.ImportPhaseReaderlist, self.ImportSfactReaderlist or self.ImportPowderReaderlist (defined in _init_Imports from the files found in the path), but in theory this list could be tailored. Used only when reader is None. :param str label: string to place on the open file dialog: Open `label` input file :param bool multiple: True if multiple files can be selected in the file dialog. False is default. At present True is used only for reading of powder data. :param list usedRanIdList: an optional list of random Ids that have been used and should not be reused :returns: a list of reader objects (rd_list) that were able to read the specified file(s). This list may be empty. ''' self.lastimport = '' self.zipfile = None if reader is None: multiple = False #print "use all formats" choices = "any file (*.*)|*.*" choices += "|zip archive (.zip)|*.zip" extdict = {} # compile a list of allowed extensions for rd in readerlist: fmt = rd.formatName for extn in rd.extensionlist: if not extdict.get(extn): extdict[extn] = [] extdict[extn] += [fmt,] for extn in sorted(extdict.keys(),cmp=lambda x,y: cmp(x.lower(), y.lower())): fmt = '' for f in extdict[extn]: if fmt != "": fmt += ', ' fmt += f choices += "|" + fmt + " file (*" + extn + ")|*" + extn else: readerlist = [reader,] # compile a list of allowed extensions choices = reader.formatName + " file (" w = "" for extn in reader.extensionlist: if w != "": w += ";" w += "*" + extn choices += w + ")|" + w choices += "|zip archive (.zip)|*.zip" if not reader.strictExtension: choices += "|any file (*.*)|*.*" # get the file(s) if multiple: mode = style=wx.OPEN | wx.CHANGE_DIR | wx.MULTIPLE else: mode = style=wx.OPEN | wx.CHANGE_DIR dlg = wx.FileDialog(self, message="Choose "+label+" input file", defaultFile="",wildcard=choices, style=mode) try: if dlg.ShowModal() == wx.ID_OK: if multiple: filelist = dlg.GetPaths() if len(filelist) == 0: return [] else: filename = dlg.GetPath() filelist = [filename,] os.chdir(dlg.GetDirectory()) # to get Mac/Linux to change directory! else: # cancel was pressed return [] finally: dlg.Destroy() rd_list = [] filelist1 = [] for filename in filelist: # is this a zip file? if os.path.splitext(filename)[1].lower() == '.zip': extractedfiles = G2IO.ExtractFileFromZip( filename,parent=self, multipleselect=True) if extractedfiles is None: continue # error or Cancel if extractedfiles != filename: self.zipfile = filename # save zip name filelist1 += extractedfiles continue filelist1.append(filename) filelist = filelist1 for filename in filelist: # is this a zip file? if os.path.splitext(filename)[1].lower() == '.zip': extractedfile = G2IO.ExtractFileFromZip(filename,parent=self) if extractedfile is None: continue # error or Cancel if extractedfile != filename: filename,self.zipfile = extractedfile,filename # now use the file that was created # set what formats are compatible with this file primaryReaders = [] secondaryReaders = [] for r in readerlist: flag = r.ExtensionValidator(filename) if flag is None: secondaryReaders.append(r) elif flag: primaryReaders.append(r) if len(secondaryReaders) + len(primaryReaders) == 0: self.ErrorDialog('No Format','No matching format for file '+filename) return [] fp = None msg = '' try: fp = open(filename,'Ur') if len(filelist) == 1: # confirm we have the right file rdmsg = 'File '+str(filename)+' begins:\n\n' for i in range(3): rdmsg += fp.readline() rdmsg += '\n\nDo you want to read this file?' if not all([ord(c) < 128 and ord(c) != 0 for c in rdmsg]): # show only if ASCII rdmsg = 'File '+str( filename)+' is a binary file. Do you want to read this file?' result = wx.ID_NO # it would be better to use something that # would resize better, but this will do for now dlg = wx.MessageDialog( self, rdmsg, 'Is this the file you want?', wx.YES_NO | wx.ICON_QUESTION, ) dlg.SetSize((700,300)) # does not resize on Mac try: result = dlg.ShowModal() finally: dlg.Destroy() if result == wx.ID_NO: return [] self.lastimport = filename # try the file first with Readers that specify the # files extension and later with ones that allow it flag = False for rd in primaryReaders+secondaryReaders: try: fp.seek(0) # rewind if not rd.ContentsValidator(fp): continue # rejected on cursory check repeat = True rdbuffer = {} # create temporary storage for file reader block = 0 while repeat: block += 1 repeat = False fp.seek(0) # rewind rd.objname = os.path.basename(filename) flag = rd.Reader(filename,fp,self, buffer=rdbuffer, blocknum=block, usedRanIdList=usedRanIdList, ) if flag: rd_list.append(copy.deepcopy(rd)) # success if rd.repeat: repeat = True except: import traceback print traceback.format_exc() msg += '\nError reading file '+filename+' with format '+ rd.formatName #self.ErrorDialog('Read Error', # 'Error reading file '+filename # +' with format '+ rd.formatName) continue if flag: if rd.warnings: self.ErrorDialog('Read Warning','The '+ rd.formatName+ ' reader reported a warning message:\n\n'+ rd.warnings) break # success reading else: if reader: self.ErrorDialog('Read Error','The '+ rd.formatName+ ' reader was not able to read file '+filename+msg) else: self.ErrorDialog('Read Error','No reader is able to read file '+filename+msg) except: import traceback print traceback.format_exc() self.ErrorDialog('Open Error','Error on open of file '+filename) if fp: fp.close() return rd_list def _Add_ImportMenu_Phase(self,parent): '''configure the Import Phase menus accord to the readers found in _init_Imports ''' submenu = wx.Menu() item = parent.AppendMenu(wx.ID_ANY, 'Phase', submenu, help='Import phase data') for reader in self.ImportPhaseReaderlist: item = submenu.Append(wx.ID_ANY,help=reader.longFormatName, kind=wx.ITEM_NORMAL,text='from '+reader.formatName+' file') self.ImportMenuId[item.GetId()] = reader self.Bind(wx.EVT_MENU, self.OnImportPhase, id=item.GetId()) item = submenu.Append(wx.ID_ANY, help='Import phase data, use file to try to determine format', kind=wx.ITEM_NORMAL, text='guess format from file') self.Bind(wx.EVT_MENU, self.OnImportPhase, id=item.GetId()) def OnImportPhase(self,event): '''Called in response to an Import/Phase/... menu item to read phase information. dict self.ImportMenuId is used to look up the specific reader item associated with the menu item, which will be None for the last menu item, which is the "guess" option where all appropriate formats will be tried. ''' # look up which format was requested reqrdr = self.ImportMenuId.get(event.GetId()) # make a list of used phase ranId's phaseRIdList = [] sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases') if sub: item, cookie = self.PatternTree.GetFirstChild(sub) while item: phaseName = self.PatternTree.GetItemText(item) ranId = self.PatternTree.GetItemPyData(item).get('ranId') if ranId: phaseRIdList.append(ranId) item, cookie = self.PatternTree.GetNextChild(sub, cookie) rdlist = self.OnImportGeneric(reqrdr, self.ImportPhaseReaderlist, 'phase',usedRanIdList=phaseRIdList) if len(rdlist) == 0: return # for now rdlist is only expected to have one element # but this will allow multiple phases to be imported self.CheckNotebook() for rd in rdlist: dlg = wx.TextEntryDialog( # allow editing of phase name self, 'Enter the name for the new phase', 'Edit phase name', rd.Phase['General']['Name'], style=wx.OK) dlg.CenterOnParent() if dlg.ShowModal() == wx.ID_OK: rd.Phase['General']['Name'] = dlg.GetValue() dlg.Destroy() PhaseName = rd.Phase['General']['Name'] print 'Read phase '+str(PhaseName)+' from file '+str(self.lastimport) if not G2gd.GetPatternTreeItemId(self,self.root,'Phases'): sub = self.PatternTree.AppendItem(parent=self.root,text='Phases') else: sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases') psub = self.PatternTree.AppendItem(parent=sub,text=PhaseName) self.PatternTree.SetItemPyData(psub,rd.Phase) self.PatternTree.Expand(self.root) # make sure phases are seen self.PatternTree.Expand(sub) self.PatternTree.Expand(psub) if rd.Constraints: sub = G2gd.GetPatternTreeItemId(self,self.root,'Constraints') # was created in CheckNotebook if needed Constraints = self.PatternTree.GetItemPyData(sub) # TODO: make sure that NEWVAR names are unique here? for i in rd.Constraints: if type(i) is dict: #for j in i: print j,' --> ',i[j] if '_Explain' not in Constraints: Constraints['_Explain'] = {} Constraints['_Explain'].update(i) continue Constraints['Phase'].append(i) return # success def _Add_ImportMenu_Sfact(self,parent): '''configure the Import Structure Factor menus accord to the readers found in _init_Imports ''' submenu = wx.Menu() item = parent.AppendMenu(wx.ID_ANY, 'Structure Factor', submenu, help='Import Structure Factor data') for reader in self.ImportSfactReaderlist: item = submenu.Append(wx.ID_ANY,help=reader.longFormatName, kind=wx.ITEM_NORMAL,text='from '+reader.formatName+' file') self.ImportMenuId[item.GetId()] = reader self.Bind(wx.EVT_MENU, self.OnImportSfact, id=item.GetId()) item = submenu.Append(wx.ID_ANY, help='Import Structure Factor, use file to try to determine format', kind=wx.ITEM_NORMAL, text='guess format from file') self.Bind(wx.EVT_MENU, self.OnImportSfact, id=item.GetId()) def OnImportSfact(self,event): '''Called in response to an Import/Structure Factor/... menu item to read single crystal datasets. dict self.ImportMenuId is used to look up the specific reader item associated with the menu item, which will be None for the last menu item, which is the "guess" option where all appropriate formats will be tried. ''' # look up which format was requested reqrdr = self.ImportMenuId.get(event.GetId()) rdlist = self.OnImportGeneric(reqrdr,self.ImportSfactReaderlist, 'Structure Factor') if len(rdlist) == 0: return self.CheckNotebook() for rd in rdlist: HistName = rd.objname if len(rdlist) <= 2: dlg = wx.TextEntryDialog( # allow editing of Structure Factor name self, 'Enter the name for the new Structure Factor', 'Edit Structure Factor name', HistName, style=wx.OK) dlg.CenterOnParent() if dlg.ShowModal() == wx.ID_OK: HistName = dlg.GetValue() dlg.Destroy() print 'Read structure factor table '+str(HistName)+' from file '+str(self.lastimport) Id = self.PatternTree.AppendItem(parent=self.root, text='HKLF '+HistName) valuesdict = { 'wtFactor':1.0, 'Dummy':False, 'ranId':ran.randint(0,sys.maxint), } self.PatternTree.SetItemPyData(Id,[valuesdict,rd.RefDict]) Sub = self.PatternTree.AppendItem(Id,text='Instrument Parameters') self.PatternTree.SetItemPyData(Sub,rd.Parameters) self.PatternTree.SetItemPyData( self.PatternTree.AppendItem(Id,text='HKL Plot Controls'), rd.Controls) self.PatternTree.SetItemPyData( self.PatternTree.AppendItem(Id,text='Reflection List'),[]) #dummy entry for GUI use self.PatternTree.SelectItem(Id) self.PatternTree.Expand(Id) self.Sngl = Id return # success def _Add_ImportMenu_powder(self,parent): '''configure the Powder Data menus accord to the readers found in _init_Imports ''' submenu = wx.Menu() item = parent.AppendMenu(wx.ID_ANY, 'Powder Data', submenu, help='Import Powder data') for reader in self.ImportPowderReaderlist: item = submenu.Append(wx.ID_ANY,help=reader.longFormatName, kind=wx.ITEM_NORMAL,text='from '+reader.formatName+' file') self.ImportMenuId[item.GetId()] = reader self.Bind(wx.EVT_MENU, self.OnImportPowder, id=item.GetId()) item = submenu.Append(wx.ID_ANY, help='Import powder data, use file to try to determine format', kind=wx.ITEM_NORMAL,text='guess format from file') self.Bind(wx.EVT_MENU, self.OnImportPowder, id=item.GetId()) submenu.AppendSeparator() item = submenu.Append(wx.ID_ANY, help='Create a powder data set entry that will be simulated', kind=wx.ITEM_NORMAL,text='Simulate a dataset') self.Bind(wx.EVT_MENU, self.OnDummyPowder, id=item.GetId()) def ReadPowderInstprm(self,instfile): #fix the write routine for [inst1,inst2] style '''Read a GSAS-II (new) instrument parameter file :param str instfile: name of instrument parameter file ''' if os.path.splitext(instfile)[1].lower() != '.instprm': # invalid file return None if not os.path.exists(instfile): # no such file return None File = open(instfile,'r') S = File.readline() if not S.startswith('#GSAS-II'): # not a valid file File.close() return None newItems = [] newVals = [] while S: if S[0] == '#': S = File.readline() continue [item,val] = S[:-1].split(':') newItems.append(item) try: newVals.append(float(val)) except ValueError: newVals.append(val) S = File.readline() File.close() # add a second MT dict here. TOF parms? (BHT) return G2IO.makeInstDict(newItems,newVals,len(newVals)*[False,]),{} def ReadPowderIparm(self,instfile,bank,databanks,rd): '''Read a GSAS (old) instrument parameter file :param str instfile: name of instrument parameter file :param int bank: the bank number read in the raw data file :param int databanks: the number of banks in the raw data file. If the number of banks in the data and instrument parameter files agree, then the sets of banks are assumed to match up and bank is used to select the instrument parameter file. If not, the user is asked to make a selection. :param obj rd: the raw data (histogram) data object. This sets rd.instbank. ''' if not os.path.exists(instfile): # no such file return {} fp = 0 try: fp = open(instfile,'Ur') Iparm = {} for S in fp: Iparm[S[:12]] = S[12:-1] except IOError: print('Error reading file:'+str(instfile)) if fp: fp.close() ibanks = int(Iparm.get('INS BANK ','1').strip()) hType = Iparm['INS HTYPE '].strip() if ibanks == 1: # there is only one bank here, return it rd.instbank = 1 return Iparm if 'PNT' in hType: rd.instbank = bank elif ibanks != databanks: # number of banks in data and prm file not not agree, need a # choice from a human here choices = [] for i in range(1,1+ibanks): choices.append('Bank '+str(i)) bank = rd.BlockSelector( choices, self, title='Select an instrument parameter bank for '+ os.path.split(rd.powderentry[0])[1]+' BANK '+str(bank)+ '\nOr use Cancel to select from the default parameter sets', header='Block Selector') if bank is None: return {} # pull out requested bank # bank from the data, and change the bank to 1 IparmS = {} for key in Iparm: if key[4:6] == " ": IparmS[key] = Iparm[key] elif int(key[4:6].strip()) == bank: IparmS[key[:4]+' 1'+key[6:]] = Iparm[key] rd.instbank = bank return IparmS def GetPowderIparm(self,rd, prevIparm, lastIparmfile, lastdatafile): '''Open and read an instrument parameter file for a data file Returns the list of parameters used in the data tree :param obj rd: the raw data (histogram) data object. :param str prevIparm: not used :param str lastIparmfile: Name of last instrument parameter file that was read, or a empty string. :param str lastdatafile: Name of last data file that was read. :returns: a list of two dicts, the first containing instrument parameters and the second used for future TOF datasets (timemaps?) ''' def SetPowderInstParms(Iparm, rd): '''extracts values from instrument parameters in rd.instdict or in array Iparm. Create and return the contents of the instrument parameter tree entry. ''' DataType = Iparm['INS HTYPE '].strip()[:3] # take 1st 3 chars # override inst values with values read from data file if rd.instdict.get('type'): DataType = rd.instdict.get('type') data = [DataType,] instname = Iparm.get('INS 1INAME ') if instname: rd.Sample['InstrName'] = instname.strip() if 'C' in DataType: wave1 = None wave2 = 0.0 if rd.instdict.get('wave'): wl = rd.instdict.get('wave') wave1 = wl[0] if len(wl) > 1: wave2 = wl[1] s = Iparm['INS 1 ICONS'] if not wave1: wave1 = G2IO.sfloat(s[:10]) wave2 = G2IO.sfloat(s[10:20]) v = (wave1,wave2, G2IO.sfloat(s[20:30]),G2IO.sfloat(s[55:65]),G2IO.sfloat(s[40:50])) #get lam1, lam2, zero, pola & ratio if not v[1]: names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth'] v = (v[0],v[2],v[4]) codes = [0,0,0,0] else: names = ['Type','Lam1','Lam2','Zero','I(L2)/I(L1)','Polariz.','U','V','W','X','Y','SH/L','Azimuth'] codes = [0,0,0,0,0,0] data.extend(v) v1 = Iparm['INS 1PRCF1 '].split() v = Iparm['INS 1PRCF11'].split() data.extend([float(v[0]),float(v[1]),float(v[2])]) #get GU, GV & GW - always here azm = float(Iparm.get('INS 1DETAZM','0.0')) v = Iparm['INS 1PRCF12'].split() if v1[0] == 3: data.extend([float(v[0]),float(v[1]),float(v[2])+float(v[3],azm)]) #get LX, LY, S+H/L & azimuth else: data.extend([0.0,0.0,0.002,azm]) #OK defaults if fxn #3 not 1st in iprm file codes.extend([0,0,0,0,0,0,0]) return [G2IO.makeInstDict(names,data,codes),{}] elif 'T' in DataType: names = ['Type','2-theta','difC','difA','Zero','alpha','beta-0','beta-1', 'beta-q','sig-0','sig-1','sig-q','X','Y','Azimuth'] codes = [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0] azm = 0. if 'INS 1DETAZM' in Iparm: azm = float(Iparm['INS 1DETAZM']) s = Iparm['INS 1BNKPAR'].split() data.extend([G2IO.sfloat(s[1]),]) #2-theta for bank s = Iparm['INS 1 ICONS'].split() data.extend([G2IO.sfloat(s[0]),G2IO.sfloat(s[1]),G2IO.sfloat(s[2])]) #difC, difA, Zero s = Iparm['INS 1PRCF1 '].split() pfType = int(s[0]) s = Iparm['INS 1PRCF11'].split() if abs(pfType) == 1: data.extend([G2IO.sfloat(s[1]),G2IO.sfloat(s[2]),G2IO.sfloat(s[3])]) s = Iparm['INS 1PRCF12'].split() data.extend([0.0,0.0,G2IO.sfloat(s[1]),0.0,0.0,0.0,azm]) elif abs(pfType) in [3,4,5]: data.extend([G2IO.sfloat(s[0]),G2IO.sfloat(s[1]),G2IO.sfloat(s[2])]) if abs(pfType) == 4: data.extend([0.0,0.0,G2IO.sfloat(s[3]),0.0,0.0,0.0,azm]) else: s = Iparm['INS 1PRCF12'].split() data.extend([0.0,0.0,G2IO.sfloat(s[0]),0.0,0.0,0.0,azm]) Inst1 = G2IO.makeInstDict(names,data,codes) Inst2 = {} if pfType < 0: Ipab = 'INS 1PAB'+str(-pfType) Npab = int(Iparm[Ipab+' '].strip()) Inst2['Pdabc'] = [] for i in range(Npab): k = Ipab+str(i+1).rjust(2) s = Iparm[k].split() Inst2['Pdabc'].append([float(t) for t in s]) Inst2['Pdabc'] = np.array(Inst2['Pdabc']) Inst2['Pdabc'].T[3] += Inst2['Pdabc'].T[0]*Inst1['difC'][0] #turn 3rd col into TOF if 'INS 1I ITYP' in Iparm: s = Iparm['INS 1I ITYP'].split() Ityp = int(s[0]) Tminmax = [float(s[1])*1000.,float(s[2])*1000.] Itypes = ['Exponential','Maxwell/Exponential','','Maxwell/Chebyschev',''] if Ityp in [1,2,4]: Inst2['Itype'] = Itypes[Ityp-1] Inst2['Tminmax'] = Tminmax Icoeff = [] Iesd = [] Icovar = [] for i in range(3): s = Iparm['INS 1ICOFF'+str(i+1)].split() Icoeff += [float(S) for S in s] s = Iparm['INS 1IECOF'+str(i+1)].split() Iesd += [float(S) for S in s] for i in range(8): s = Iparm['INS 1IECOR'+str(i+1)].split() Icovar += [float(S) for S in s] Inst2['Icoeff'] = Icoeff Inst2['Iesd'] = Iesd Inst2['Icovar'] = Icovar return [Inst1,Inst2] # stuff we might need from the reader filename = rd.powderentry[0] bank = rd.powderentry[2] numbanks = rd.numbanks # is there an instrument parameter file defined for the current data set? if rd.instparm or (lastdatafile == filename and lastIparmfile): if rd.instparm: instfile = os.path.join(os.path.split(filename)[0], rd.instparm) else: # for multiple reads of one data file, reuse the inst parm file instfile = lastIparmfile if os.path.exists(instfile): #print 'debug: try read',instfile instParmList = self.ReadPowderInstprm(instfile) if instParmList is not None: rd.instfile = instfile rd.instmsg = 'GSAS-II file '+instfile return instParmList Iparm = self.ReadPowderIparm(instfile,bank,numbanks,rd) if Iparm: #print 'debug: success' rd.instfile = instfile rd.instmsg = instfile + ' bank ' + str(rd.instbank) return SetPowderInstParms(Iparm,rd) else: self.ErrorDialog('Open Error','Error opening instrument parameter file ' +str(instfile)+' requested by file '+ filename) # is there an instrument parameter file matching the current file # with extension .inst or .prm? If so read it basename = os.path.splitext(filename)[0] for ext in '.instprm','.prm','.inst','.ins': instfile = basename + ext instParmList = self.ReadPowderInstprm(instfile) if instParmList is not None: rd.instfile = instfile rd.instmsg = 'GSAS-II file '+instfile return instParmList Iparm = self.ReadPowderIparm(instfile,bank,numbanks,rd) if Iparm: #print 'debug: success' rd.instfile = instfile rd.instmsg = instfile + ' bank ' + str(rd.instbank) return SetPowderInstParms(Iparm,rd) else: #print 'debug: open/read failed',instfile pass # fail silently # did we read the data file from a zip? If so, look there for a # instrument parameter file if self.zipfile: for ext in '.instprm','.prm','.inst','.ins': instfile = G2IO.ExtractFileFromZip( self.zipfile, selection=os.path.split(basename + ext)[1], parent=self) if instfile is not None and instfile != self.zipfile: print 'debug:',instfile,'created from ',self.zipfile instParmList = self.ReadPowderInstprm(instfile) if instParmList is not None: rd.instfile = instfile rd.instmsg = 'GSAS-II file '+instfile return instParmList Iparm = self.ReadPowderIparm(instfile,bank,numbanks,rd) if Iparm: rd.instfile = instfile rd.instmsg = instfile + ' bank ' + str(rd.instbank) return SetPowderInstParms(Iparm,rd) else: #print 'debug: open/read for',instfile,'from',self.zipfile,'failed' pass # fail silently while True: # loop until we get a file that works or we get a cancel instfile = '' dlg = wx.FileDialog( self, 'Choose inst. param file for "' +rd.idstring +'" (or Cancel for default)', '.', '', 'GSAS iparm file (*.prm,*.inst,*.ins)|*.prm;*.inst;*.ins|' 'GSAS-II iparm file (*.instprm)|*.instprm|' 'All files (*.*)|*.*', wx.OPEN|wx.CHANGE_DIR) if os.path.exists(lastIparmfile): dlg.SetFilename(lastIparmfile) if dlg.ShowModal() == wx.ID_OK: instfile = dlg.GetPath() dlg.Destroy() if not instfile: break instParmList = self.ReadPowderInstprm(instfile) if instParmList is not None: rd.instfile = instfile rd.instmsg = 'GSAS-II file '+instfile return instParmList Iparm = self.ReadPowderIparm(instfile,bank,numbanks,rd) if Iparm: #print 'debug: success with',instfile rd.instfile = instfile rd.instmsg = instfile + ' bank ' + str(rd.instbank) return SetPowderInstParms(Iparm,rd) else: self.ErrorDialog('Read Error', 'Error opening/reading file '+str(instfile)) # still no success: offer user choice of defaults while True: # loop until we get a choice choices = [] head = 'Select from default instrument parameters for '+rd.idstring for l in rd.defaultIparm_lbl: choices.append('Defaults for '+l) res = rd.BlockSelector( choices, ParentFrame=self, title=head, header='Select default inst parms', useCancel=False) if res is None: continue rd.instfile = '' rd.instmsg = 'default: '+rd.defaultIparm_lbl[res] return SetPowderInstParms(rd.defaultIparms[res],rd) def OnImportPowder(self,event): '''Called in response to an Import/Powder Data/... menu item to read a powder diffraction data set. dict self.ImportMenuId is used to look up the specific reader item associated with the menu item, which will be None for the last menu item, which is the "guess" option where all appropriate formats will be tried. Also reads an instrument parameter file for each dataset. ''' reqrdr = self.ImportMenuId.get(event.GetId()) # look up which format was requested rdlist = self.OnImportGeneric( reqrdr,self.ImportPowderReaderlist,'Powder Data',multiple=True) if len(rdlist) == 0: return self.CheckNotebook() Iparm = None lastIparmfile = '' lastdatafile = '' for rd in rdlist: # get instrument parameters for each dataset Iparm1,Iparm2 = self.GetPowderIparm(rd, Iparm, lastIparmfile, lastdatafile) if rd.repeat_instparm: lastIparmfile = rd.instfile lastdatafile = rd.powderentry[0] print 'Read powder data '+str(rd.idstring)+ \ ' from file '+str(self.lastimport) + \ ' with parameters from '+str(rd.instmsg) # data are read, now store them in the tree Id = self.PatternTree.AppendItem(parent=self.root, text='PWDR '+rd.idstring) if 'T' in Iparm1['Type'][0]: if not rd.clockWd and rd.GSAS: rd.powderdata[0] *= 100. #put back the CW centideg correction cw = np.diff(rd.powderdata[0]) rd.powderdata[0] = rd.powderdata[0][:-1]+cw/2. rd.powderdata[1] = rd.powderdata[1][:-1]/cw rd.powderdata[2] = rd.powderdata[2][:-1]*cw**2 #1/var=w at this point if 'Itype' in Iparm2: Ibeg = np.searchsorted(rd.powderdata[0],Iparm2['Tminmax'][0]) Ifin = np.searchsorted(rd.powderdata[0],Iparm2['Tminmax'][1]) rd.powderdata[0] = rd.powderdata[0][Ibeg:Ifin] YI,WYI = G2pwd.calcIncident(Iparm2,rd.powderdata[0]) rd.powderdata[1] = rd.powderdata[1][Ibeg:Ifin]/YI var = 1./rd.powderdata[2][Ibeg:Ifin] var += WYI*rd.powderdata[1]**2 var /= YI**2 rd.powderdata[2] = 1./var rd.powderdata[3] = np.zeros_like(rd.powderdata[0]) rd.powderdata[4] = np.zeros_like(rd.powderdata[0]) rd.powderdata[5] = np.zeros_like(rd.powderdata[0]) Tmin = min(rd.powderdata[0]) Tmax = max(rd.powderdata[0]) valuesdict = { 'wtFactor':1.0, 'Dummy':False, 'ranId':ran.randint(0,sys.maxint), } rd.Sample['ranId'] = valuesdict['ranId'] # this should be removed someday self.PatternTree.SetItemPyData(Id,[valuesdict,rd.powderdata]) self.PatternTree.SetItemPyData( self.PatternTree.AppendItem(Id,text='Comments'), rd.comments) self.PatternTree.SetItemPyData( self.PatternTree.AppendItem(Id,text='Limits'), [(Tmin,Tmax),[Tmin,Tmax]]) self.PatternId = G2gd.GetPatternTreeItemId(self,Id,'Limits') self.PatternTree.SetItemPyData( self.PatternTree.AppendItem(Id,text='Background'), [['chebyschev',True,3,1.0,0.0,0.0], {'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}]) self.PatternTree.SetItemPyData( self.PatternTree.AppendItem(Id,text='Instrument Parameters'), [Iparm1,Iparm2]) self.PatternTree.SetItemPyData( self.PatternTree.AppendItem(Id,text='Sample Parameters'), rd.Sample) self.PatternTree.SetItemPyData( self.PatternTree.AppendItem(Id,text='Peak List') ,[]) self.PatternTree.SetItemPyData( self.PatternTree.AppendItem(Id,text='Index Peak List'), []) self.PatternTree.SetItemPyData( self.PatternTree.AppendItem(Id,text='Unit Cells List'), []) self.PatternTree.SetItemPyData( self.PatternTree.AppendItem(Id,text='Reflection Lists'), {}) self.PatternTree.Expand(Id) self.PatternTree.SelectItem(Id) return # success def OnDummyPowder(self,event): '''Called in response to Import/Powder Data/Simulate menu item to create a Dummy powder diffraction data set. Reads an instrument parameter file and then gets input from the user ''' rd = G2IO.ImportPowderData( extensionlist=tuple(), strictExtension=False, formatName = 'Simulate dataset', longFormatName = 'Compute a simulated pattern') rd.powderentry[0] = '' # no filename # #self.powderentry[1] = pos # bank offset (N/A here) rd.powderentry[2] = 1 # only one bank rd.comments.append('This is a dummy dataset for powder pattern simulation') self.CheckNotebook() Iparm = None lastIparmfile = '' lastdatafile = '' self.zipfile = None # get instrument parameters for Iparm1,Iparm2 = self.GetPowderIparm(rd, Iparm, lastIparmfile, lastdatafile) if 'T' in Iparm1['Type'][0]: print('TOF simulation not supported yet') return False else: # need to get name, 2theta start, end, step rd.idstring = ' CW' if 'X' in Iparm1['Type'][0]: rd.idstring = 'CW x-ray simulation' else: rd.idstring = 'CW neutron simulation' # base initial range on wavelength wave = Iparm1.get('Lam') if wave: wave = wave[0] else: wave = Iparm1.get('Lam1') if wave: wave = wave[0] N = 0 while (N < 3): # insist on a dataset with a few points names = ('dataset name', 'start angle', 'end angle', 'step size') if not wave or wave < 1.0: inp = [rd.idstring, 10.,40.,0.005] # see names for what's what else: inp = [rd.idstring, 10.,80.,0.01] # see names for what's what dlg = G2gd.ScrolledMultiEditor( self,[inp] * len(inp),range(len(inp)),names, header='Enter simulation name and range', minvals=(None,0.001,0.001,0.0001), maxvals=(None,180.,180.,.1), sizevals=((225,-1),) ) dlg.CenterOnParent() if dlg.ShowModal() == wx.ID_OK: if inp[1] > inp[2]: end,start,step = inp[1:] else: start,end,step = inp[1:] step = abs(step) else: return False N = int((end-start)/step)+1 x = np.linspace(start,end,N,True) N = len(x) rd.powderdata = [ np.array(x), # x-axis values np.zeros_like(x), # powder pattern intensities np.ones_like(x), # 1/sig(intensity)^2 values (weights) np.zeros_like(x), # calc. intensities (zero) np.zeros_like(x), # calc. background (zero) np.zeros_like(x), # obs-calc profiles ] Tmin = rd.powderdata[0][0] Tmax = rd.powderdata[0][-1] # data are read, now store them in the tree Id = self.PatternTree.AppendItem(parent=self.root, text='PWDR '+inp[0]) valuesdict = { 'wtFactor':1.0, 'Dummy':True, 'ranId':ran.randint(0,sys.maxint), } self.PatternTree.SetItemPyData(Id,[valuesdict,rd.powderdata]) self.PatternTree.SetItemPyData( self.PatternTree.AppendItem(Id,text='Comments'), rd.comments) self.PatternTree.SetItemPyData( self.PatternTree.AppendItem(Id,text='Limits'), [(Tmin,Tmax),[Tmin,Tmax]]) self.PatternId = G2gd.GetPatternTreeItemId(self,Id,'Limits') self.PatternTree.SetItemPyData( self.PatternTree.AppendItem(Id,text='Background'), [['chebyschev',True,3,1.0,0.0,0.0], {'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}]) self.PatternTree.SetItemPyData( self.PatternTree.AppendItem(Id,text='Instrument Parameters'), [Iparm1,Iparm2]) self.PatternTree.SetItemPyData( self.PatternTree.AppendItem(Id,text='Sample Parameters'), rd.Sample) self.PatternTree.SetItemPyData( self.PatternTree.AppendItem(Id,text='Peak List') ,[]) self.PatternTree.SetItemPyData( self.PatternTree.AppendItem(Id,text='Index Peak List'), []) self.PatternTree.SetItemPyData( self.PatternTree.AppendItem(Id,text='Unit Cells List'), []) self.PatternTree.SetItemPyData( self.PatternTree.AppendItem(Id,text='Reflection Lists'), {}) self.PatternTree.Expand(Id) self.PatternTree.SelectItem(Id) print('Added simulation powder data '+str(rd.idstring)+ ' with parameters from '+str(rd.instmsg)) return # success def _init_Exports(self,menu): '''Find exporter routines and add them into menus ''' # set up the top-level menus projectmenu = wx.Menu() item = menu.AppendMenu( wx.ID_ANY, 'Entire project as', projectmenu, help='Export entire project') phasemenu = wx.Menu() item = menu.AppendMenu( wx.ID_ANY, 'Phase as', phasemenu, help='Export phase or sometimes phases') powdermenu = wx.Menu() item = menu.AppendMenu( wx.ID_ANY, 'Powder data as', powdermenu, help='Export powder diffraction histogram(s)') singlemenu = wx.Menu() item = menu.AppendMenu( wx.ID_ANY, 'Single crystal data as', singlemenu, help='Export single crystal histogram(s)') imagemenu = wx.Menu() item = menu.AppendMenu( wx.ID_ANY, 'Images as', imagemenu, help='Export powder image(s)') mapmenu = wx.Menu() item = menu.AppendMenu( wx.ID_ANY, 'Maps as', mapmenu, help='Export density map(s)') # pdfmenu = wx.Menu() # item = menu.AppendMenu( # wx.ID_ANY, 'PDFs as', # pdfmenu, help='Export pair distribution function(s)') # find all the exporter files pathlist = sys.path filelist = [] for path in pathlist: for filename in glob.iglob(os.path.join( path, "G2export*.py")): filelist.append(filename) filelist = sorted(list(set(filelist))) # remove duplicates exporterlist = [] # go through the routines and import them, saving objects that # have export routines (method Exporter) for filename in filelist: path,rootname = os.path.split(filename) pkg = os.path.splitext(rootname)[0] try: fp = None fp, fppath,desc = imp.find_module(pkg,[path,]) pkg = imp.load_module(pkg,fp,fppath,desc) for clss in inspect.getmembers(pkg): # find classes defined in package if clss[0].startswith('_'): continue if inspect.isclass(clss[1]): # check if we have the required methods for m in 'Exporter','loadParmDict': if not hasattr(clss[1],m): break if not callable(getattr(clss[1],m)): break else: exporter = clss[1](self) # create an export instance exporterlist.append(exporter) except AttributeError: print 'Import_'+errprefix+': Attribute Error'+str(filename) pass except ImportError: print 'Import_'+errprefix+': Error importing file'+str(filename) pass if fp: fp.close() # Add submenu item(s) for each Exporter by its self-declared type (can be more than one) for obj in exporterlist: #print 'exporter',obj for typ in obj.exporttype: if typ == "project": submenu = projectmenu elif typ == "phase": submenu = phasemenu elif typ == "powder": submenu = powdermenu elif typ == "single": submenu = singlemenu elif typ == "image": submenu = imagemenu elif typ == "map": submenu = mapmenu # elif typ == "pdf": # submenu = pdfmenu else: print("Error, unknown type in "+str(obj)) break item = submenu.Append( wx.ID_ANY, help=obj.longFormatName, kind=wx.ITEM_NORMAL, text=obj.formatName) self.Bind(wx.EVT_MENU, obj.Exporter, id=item.GetId()) self.ExportLookup[item.GetId()] = typ # lookup table for submenu item #code to debug an Exporter. much is hard-coded below, but code is reloaded before # each use allowing faster development # def DebugExport(event): # print 'start reload' # reload(G2IO) # import G2export_ASCIImap as dev # reload(dev) # dev.ExportMapASCII(self).Exporter(event) # item = menu.Append( # wx.ID_ANY,kind=wx.ITEM_NORMAL, # help="debug exporter",text="test Export") # self.Bind(wx.EVT_MENU, DebugExport, id=item.GetId()) # #self.ExportLookup[item.GetId()] = 'image' # self.ExportLookup[item.GetId()] = 'map' def _Add_ExportMenuItems(self,parent): item = parent.Append( help='Select PWDR item to enable',id=wx.ID_ANY, kind=wx.ITEM_NORMAL, text='Export Powder Patterns...') self.ExportPattern.append(item) item.Enable(False) self.Bind(wx.EVT_MENU, self.OnExportPatterns, id=item.GetId()) item = parent.Append( help='',id=wx.ID_ANY, kind=wx.ITEM_NORMAL, text='Export All Peak Lists...') self.ExportPeakList.append(item) item.Enable(True) self.Bind(wx.EVT_MENU, self.OnExportPeakList, id=item.GetId()) item = parent.Append( help='',id=wx.ID_ANY, kind=wx.ITEM_NORMAL, text='Export HKLs...') self.ExportHKL.append(item) self.Bind(wx.EVT_MENU, self.OnExportHKL, id=item.GetId()) item = parent.Append( help='Select PDF item to enable', id=wx.ID_ANY, kind=wx.ITEM_NORMAL, text='Export PDF...') self.ExportPDF.append(item) item.Enable(False) self.Bind(wx.EVT_MENU, self.OnExportPDF, id=item.GetId()) def FillMainMenu(self,menubar): '''Define contents of the main GSAS-II menu for the (main) data tree window in the mac, used also for the data item windows as well. ''' File = wx.Menu(title='') menubar.Append(menu=File, title='&File') self._Add_FileMenuItems(File) Data = wx.Menu(title='') menubar.Append(menu=Data, title='Data') self._Add_DataMenuItems(Data) Calculate = wx.Menu(title='') menubar.Append(menu=Calculate, title='&Calculate') self._Add_CalculateMenuItems(Calculate) Import = wx.Menu(title='') menubar.Append(menu=Import, title='Import') self._Add_ImportMenu_Phase(Import) self._Add_ImportMenu_powder(Import) self._Add_ImportMenu_Sfact(Import) #====================================================================== # Code to help develop/debug an importer, much is hard-coded below # but module is reloaded before each use, allowing faster testing # def DebugImport(event): # print 'start reload' # import G2phase_ISO as dev # reload(dev) # rd = dev.ISODISTORTPhaseReader() # self.ImportMenuId[event.GetId()] = rd # self.OnImportPhase(event) # or ---------------------------------------------------------------------- #self.OnImportGeneric(rd,[],'test of ISODISTORTPhaseReader') # special debug code # or ---------------------------------------------------------------------- # filename = '/Users/toby/projects/branton/subgroup_cif.txt' # fp = open(filename,'Ur') # if not rd.ContentsValidator(fp): # print 'not validated' # # make a list of used phase ranId's # phaseRIdList = [] # sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases') # if sub: # item, cookie = self.PatternTree.GetFirstChild(sub) # while item: # phaseName = self.PatternTree.GetItemText(item) # ranId = self.PatternTree.GetItemPyData(item).get('ranId') # if ranId: phaseRIdList.append(ranId) # item, cookie = self.PatternTree.GetNextChild(sub, cookie) # if rd.Reader(filename,fp,usedRanIdList=phaseRIdList): # print 'read OK' # item = Import.Append( # wx.ID_ANY,kind=wx.ITEM_NORMAL, # help="debug importer",text="test importer") # self.Bind(wx.EVT_MENU, DebugImport, id=item.GetId()) #====================================================================== self.ExportMenu = wx.Menu(title='') menubar.Append(menu=self.ExportMenu, title='Export') self._init_Exports(self.ExportMenu) self._Add_ExportMenuItems(self.ExportMenu) HelpMenu=G2gd.MyHelp(self,helpType='Data tree', morehelpitems=[('&Tutorials','Tutorials')]) menubar.Append(menu=HelpMenu,title='&Help') def _init_ctrls(self, parent): wx.Frame.__init__(self, name='GSASII', parent=parent, size=wx.Size(400, 250),style=wx.DEFAULT_FRAME_STYLE, title='GSAS-II data tree') clientSize = wx.ClientDisplayRect() Size = self.GetSize() xPos = clientSize[2]-Size[0] self.SetPosition(wx.Point(xPos,clientSize[1])) self._init_Imports() #initialize Menu item objects (these contain lists of menu items that are enabled or disabled) self.MakePDF = [] self.Refine = [] self.SeqRefine = [] self.ExportPattern = [] self.ExportPeakList = [] self.ExportHKL = [] self.ExportPDF = [] self.ExportPhase = [] self.ExportCIF = [] # self.GSASIIMenu = wx.MenuBar() self.FillMainMenu(self.GSASIIMenu) self.SetMenuBar(self.GSASIIMenu) self.Bind(wx.EVT_SIZE, self.OnSize) self.CreateStatusBar() self.mainPanel = wx.Panel(self,-1) wxID_PATTERNTREE = wx.NewId() self.PatternTree = wx.TreeCtrl(id=wxID_PATTERNTREE, parent=self.mainPanel, pos=wx.Point(0, 0),style=wx.TR_DEFAULT_STYLE ) self.PatternTree.Bind(wx.EVT_TREE_SEL_CHANGED, self.OnPatternTreeSelChanged, id=wxID_PATTERNTREE) self.PatternTree.Bind(wx.EVT_TREE_ITEM_COLLAPSED, self.OnPatternTreeItemCollapsed, id=wxID_PATTERNTREE) self.PatternTree.Bind(wx.EVT_TREE_ITEM_EXPANDED, self.OnPatternTreeItemExpanded, id=wxID_PATTERNTREE) self.PatternTree.Bind(wx.EVT_TREE_DELETE_ITEM, self.OnPatternTreeItemDelete, id=wxID_PATTERNTREE) self.PatternTree.Bind(wx.EVT_TREE_KEY_DOWN, self.OnPatternTreeKeyDown, id=wxID_PATTERNTREE) self.root = self.PatternTree.AddRoot('Loaded Data: ') plotFrame = wx.Frame(None,-1,'GSASII Plots',size=wx.Size(700,600), \ style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX) self.G2plotNB = G2plt.G2PlotNoteBook(plotFrame) plotFrame.Show() self.dataDisplay = None def __init__(self, parent): self.ExportLookup = {} self._init_ctrls(parent) self.Image = wx.Image( os.path.join(GSASIIpath.path2GSAS2,'gsas2.ico'), wx.BITMAP_TYPE_ICO) if "wxMSW" in wx.PlatformInfo: img = self.Image.Scale(16, 16).ConvertToBitmap() elif "wxGTK" in wx.PlatformInfo: img = self.Image.Scale(22, 22).ConvertToBitmap() else: img = self.Image.ConvertToBitmap() self.SetIcon(wx.IconFromBitmap(img)) self.Bind(wx.EVT_CLOSE, self.ExitMain) # various defaults self.oldFocus = None self.GSASprojectfile = '' self.dirname = os.path.expanduser('~') #start in the users home directory by default; may be meaningless self.undofile = '' self.TreeItemDelete = False self.Offset = [0.0,0.0] self.delOffset = .02 self.refOffset = -100.0 self.refDelt = .01 self.Weight = False self.IparmName = '' # to be removed when SelectPowderData & GetInstrumentFile is self.IfPlot = False self.PatternId = 0 self.PickId = 0 self.PeakTable = [] self.LimitsTable = [] self.HKL = [] self.Lines = [] self.itemPicked = None self.dataFrame = None self.Interpolate = 'nearest' self.ContourColor = 'Paired' self.VcovColor = 'RdYlGn' self.RamaColor = 'Blues' self.Projection = 'equal area' self.logPlot = False self.qPlot = False self.Contour = False self.Legend = False self.SinglePlot = False self.SubBack = False self.plotView = 0 self.Image = 0 self.oldImagefile = '' self.ImageZ = [] self.Integrate = 0 self.imageDefault = {} self.Sngl = 0 self.ifGetRing = False self.MaskKey = '' #trigger for making image masks arg = sys.argv if len(arg) > 1: self.GSASprojectfile = os.path.splitext(arg[1])[0]+'.gpx' self.dirname = os.path.dirname(arg[1]) if self.dirname: os.chdir(self.dirname) try: G2IO.ProjFileOpen(self) self.PatternTree.Expand(self.root) for item in self.Refine: item.Enable(True) for item in self.SeqRefine: item.Enable(True) except: print 'Error opening file',arg[1] def OnSize(self,event): 'Called when the main window is resized. Not sure why' w,h = self.GetClientSizeTuple() self.mainPanel.SetSize(wx.Size(w,h)) self.PatternTree.SetSize(wx.Size(w,h)) def OnPatternTreeSelChanged(self, event): '''Called when a data tree item is selected''' if self.TreeItemDelete: self.TreeItemDelete = False else: pltNum = self.G2plotNB.nb.GetSelection() if pltNum >= 0: #to avoid the startup with no plot! pltPage = self.G2plotNB.nb.GetPage(pltNum) pltPlot = pltPage.figure item = event.GetItem() G2gd.MovePatternTreeToGrid(self,item) if self.oldFocus: self.oldFocus.SetFocus() def OnPatternTreeItemCollapsed(self, event): 'Called when a tree item is collapsed' event.Skip() def OnPatternTreeItemExpanded(self, event): 'Called when a tree item is expanded' event.Skip() def OnPatternTreeItemDelete(self, event): 'Called when a tree item is deleted -- not sure what this does' self.TreeItemDelete = True def OnPatternTreeItemActivated(self, event): 'Called when a tree item is activated' event.Skip() def OnPatternTreeKeyDown(self,event): 'Not sure what this does' key = event.GetKeyCode() item = self.PickId if type(item) is int: return # is this the toplevel in tree? if key == wx.WXK_UP: self.oldFocus = wx.Window.FindFocus() self.PatternTree.GetPrevSibling(item) elif key == wx.WXK_DOWN: self.oldFocus = wx.Window.FindFocus() self.PatternTree.GetNextSibling(item) def OnReadPowderPeaks(self,event): 'Bound to menu Data/Read Powder Peaks -- still needed?' Cuka = 1.54052 self.CheckNotebook() dlg = wx.FileDialog(self, 'Choose file with peak list', '.', '', 'peak files (*.txt)|*.txt|All files (*.*)|*.*',wx.OPEN|wx.CHANGE_DIR) try: if dlg.ShowModal() == wx.ID_OK: self.HKL = [] self.powderfile = dlg.GetPath() comments,peaks = G2IO.GetPowderPeaks(self.powderfile) Id = self.PatternTree.AppendItem(parent=self.root,text='PKS '+os.path.basename(self.powderfile)) data = ['PKS',Cuka,0.0] names = ['Type','Lam','Zero'] codes = [0,0,0] inst = [G2IO.makeInstDict(names,data,codes),{}] self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst) self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),comments) self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Index Peak List'),peaks) self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Unit Cells List'),[]) self.PatternTree.Expand(Id) self.PatternTree.SelectItem(Id) os.chdir(dlg.GetDirectory()) # to get Mac/Linux to change directory! finally: dlg.Destroy() def OnImageRead(self,event): 'Called to read in an image in any known format' self.CheckNotebook() dlg = wx.FileDialog( self, 'Choose image files', '.', '', 'Any image file (*.edf;*.tif;*.tiff;*.mar*;*.avg;*.sum;*.img;*.G2img)|' '*.edf;*.tif;*.tiff;*.mar*;*.avg;*.sum;*.img;*.G2img;*.zip|' 'European detector file (*.edf)|*.edf|' 'Any detector tif (*.tif;*.tiff)|*.tif;*.tiff|' 'MAR file (*.mar*)|*.mar*|' 'GE Image (*.avg;*.sum)|*.avg;*.sum|' 'ADSC Image (*.img)|*.img|' 'GSAS-II Image (*.G2img)|*.G2img|' 'Zip archive (*.zip)|*.zip|' 'All files (*.*)|*.*', wx.OPEN | wx.MULTIPLE|wx.CHANGE_DIR) try: if dlg.ShowModal() == wx.ID_OK: imagefiles = dlg.GetPaths() imagefiles.sort() for imagefile in imagefiles: # if a zip file, open and extract if os.path.splitext(imagefile)[1].lower() == '.zip': extractedfile = G2IO.ExtractFileFromZip(imagefile,parent=self) if extractedfile is not None and extractedfile != imagefile: imagefile = extractedfile Comments,Data,Npix,Image = G2IO.GetImageData(self,imagefile) if Comments: Id = self.PatternTree.AppendItem(parent=self.root,text='IMG '+os.path.basename(imagefile)) self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),Comments) Imax = np.amax(Image) Imin = max(0.0,np.amin(Image)) #force positive if self.imageDefault: Data = copy.copy(self.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['DetDepth'] = 0. Data['DetDepthRef'] = False else: Data['type'] = 'PWDR' Data['color'] = 'Paired' Data['tilt'] = 0.0 Data['rotation'] = 0.0 Data['showLines'] = False Data['ring'] = [] Data['rings'] = [] Data['cutoff'] = 10 Data['pixLimit'] = 20 Data['calibdmin'] = 0.5 Data['calibskip'] = 0 Data['edgemin'] = 100000000 Data['ellipses'] = [] Data['GonioAngles'] = [0.,0.,0.] Data['DetDepth'] = 0. Data['DetDepthRef'] = False Data['calibrant'] = '' Data['IOtth'] = [2.0,5.0] Data['LRazimuth'] = [135,225] Data['azmthOff'] = 0.0 Data['outChannels'] = 2500 Data['outAzimuths'] = 1 Data['centerAzm'] = False Data['fullIntegrate'] = False Data['setRings'] = False Data['background image'] = ['',1.0] Data['setDefault'] = False Data['range'] = [(Imin,Imax),[Imin,Imax]] self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Image Controls'),Data) Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(Imin,Imax),[Imin,Imax]]} self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Masks'),Masks) self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Stress/Strain'), {'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'strain':np.zeros((3,3))}) self.PatternTree.SetItemPyData(Id,[Npix,imagefile]) self.PickId = Id self.Image = Id os.chdir(dlg.GetDirectory()) # to get Mac/Linux to change directory! self.PatternTree.SelectItem(G2gd.GetPatternTreeItemId(self,Id,'Image Controls')) #show last one finally: path = dlg.GetDirectory() # to get Mac/Linux to change directory! os.chdir(path) dlg.Destroy() def CheckNotebook(self): '''Make sure the data tree has the minimally expected controls. (BHT) correct? ''' if not G2gd.GetPatternTreeItemId(self,self.root,'Notebook'): sub = self.PatternTree.AppendItem(parent=self.root,text='Notebook') self.PatternTree.SetItemPyData(sub,['']) if not G2gd.GetPatternTreeItemId(self,self.root,'Controls'): sub = self.PatternTree.AppendItem(parent=self.root,text='Controls') self.PatternTree.SetItemPyData(sub,copy.copy(G2obj.DefaultControls)) if not G2gd.GetPatternTreeItemId(self,self.root,'Covariance'): sub = self.PatternTree.AppendItem(parent=self.root,text='Covariance') self.PatternTree.SetItemPyData(sub,{}) if not G2gd.GetPatternTreeItemId(self,self.root,'Constraints'): sub = self.PatternTree.AppendItem(parent=self.root,text='Constraints') self.PatternTree.SetItemPyData(sub,{'Hist':[],'HAP':[],'Phase':[]}) if not G2gd.GetPatternTreeItemId(self,self.root,'Restraints'): sub = self.PatternTree.AppendItem(parent=self.root,text='Restraints') self.PatternTree.SetItemPyData(sub,{}) if not G2gd.GetPatternTreeItemId(self,self.root,'Rigid bodies'): sub = self.PatternTree.AppendItem(parent=self.root,text='Rigid bodies') self.PatternTree.SetItemPyData(sub,{'Vector':{'AtInfo':{}}, 'Residue':{'AtInfo':{}},'RBIds':{'Vector':[],'Residue':[]}}) class CopyDialog(wx.Dialog): '''Creates a dialog for copying control settings between data tree items''' def __init__(self,parent,title,text,data): wx.Dialog.__init__(self,parent,-1,title, pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE) self.data = data panel = wx.Panel(self) mainSizer = wx.BoxSizer(wx.VERTICAL) topLabl = wx.StaticText(panel,-1,text) mainSizer.Add((10,10),1) mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL|wx.LEFT,10) mainSizer.Add((10,10),1) ncols = len(data)/40+1 dataGridSizer = wx.FlexGridSizer(rows=len(data),cols=ncols,hgap=2,vgap=2) for id,item in enumerate(self.data): ckbox = wx.CheckBox(panel,id,item[1]) ckbox.Bind(wx.EVT_CHECKBOX,self.OnCopyChange) dataGridSizer.Add(ckbox,0,wx.LEFT,10) mainSizer.Add(dataGridSizer,0,wx.EXPAND) OkBtn = wx.Button(panel,-1,"Ok") OkBtn.Bind(wx.EVT_BUTTON, self.OnOk) cancelBtn = wx.Button(panel,-1,"Cancel") cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel) btnSizer = wx.BoxSizer(wx.HORIZONTAL) btnSizer.Add((20,20),1) btnSizer.Add(OkBtn) btnSizer.Add((20,20),1) btnSizer.Add(cancelBtn) btnSizer.Add((20,20),1) mainSizer.Add(btnSizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP, 10) panel.SetSizer(mainSizer) panel.Fit() self.Fit() def OnCopyChange(self,event): id = event.GetId() self.data[id][0] = self.FindWindowById(id).GetValue() def OnOk(self,event): parent = self.GetParent() parent.Raise() self.EndModal(wx.ID_OK) def OnCancel(self,event): parent = self.GetParent() parent.Raise() self.EndModal(wx.ID_CANCEL) def GetData(self): return self.data class SumDialog(wx.Dialog): 'Allows user to supply scale factor(s) when summing data' def __init__(self,parent,title,text,dataType,data): wx.Dialog.__init__(self,parent,-1,title, pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE) self.data = data panel = wx.Panel(self) mainSizer = wx.BoxSizer(wx.VERTICAL) topLabl = wx.StaticText(panel,-1,text) mainSizer.Add((10,10),1) mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL|wx.LEFT,10) mainSizer.Add((10,10),1) dataGridSizer = wx.FlexGridSizer(rows=len(data),cols=2,hgap=2,vgap=2) for id,item in enumerate(self.data[:-1]): name = wx.TextCtrl(panel,-1,item[1],size=wx.Size(200,20)) name.SetEditable(False) scale = wx.TextCtrl(panel,id,'%.3f'%(item[0]),style=wx.TE_PROCESS_ENTER) scale.Bind(wx.EVT_TEXT_ENTER,self.OnScaleChange) scale.Bind(wx.EVT_KILL_FOCUS,self.OnScaleChange) dataGridSizer.Add(scale,0,wx.LEFT,10) dataGridSizer.Add(name,0,wx.RIGHT,10) if dataType: dataGridSizer.Add(wx.StaticText(panel,-1,'Sum result name: '+dataType),0, \ wx.LEFT|wx.TOP|wx.ALIGN_CENTER_VERTICAL,10) self.name = wx.TextCtrl(panel,-1,self.data[-1],size=wx.Size(200,20),style=wx.TE_PROCESS_ENTER) self.name.Bind(wx.EVT_TEXT_ENTER,self.OnNameChange) self.name.Bind(wx.EVT_KILL_FOCUS,self.OnNameChange) dataGridSizer.Add(self.name,0,wx.RIGHT|wx.TOP,10) mainSizer.Add(dataGridSizer,0,wx.EXPAND) OkBtn = wx.Button(panel,-1,"Ok") OkBtn.Bind(wx.EVT_BUTTON, self.OnOk) cancelBtn = wx.Button(panel,-1,"Cancel") cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel) btnSizer = wx.BoxSizer(wx.HORIZONTAL) btnSizer.Add((20,20),1) btnSizer.Add(OkBtn) btnSizer.Add((20,20),1) btnSizer.Add(cancelBtn) btnSizer.Add((20,20),1) mainSizer.Add(btnSizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP, 10) panel.SetSizer(mainSizer) panel.Fit() self.Fit() def OnScaleChange(self,event): id = event.GetId() value = self.FindWindowById(id).GetValue() try: self.data[id][0] = float(value) self.FindWindowById(id).SetValue('%.3f'%(self.data[id][0])) except ValueError: if value and '-' not in value[0]: print 'bad input - numbers only' self.FindWindowById(id).SetValue('0.000') def OnNameChange(self,event): self.data[-1] = self.name.GetValue() def OnOk(self,event): parent = self.GetParent() parent.Raise() self.EndModal(wx.ID_OK) def OnCancel(self,event): parent = self.GetParent() parent.Raise() self.EndModal(wx.ID_CANCEL) def GetData(self): return self.data def OnPwdrSum(self,event): 'Sum together powder data(?)' TextList = [] DataList = [] SumList = [] Names = [] Inst = None SumItemList = [] Comments = ['Sum equals: \n'] if self.PatternTree.GetCount(): item, cookie = self.PatternTree.GetFirstChild(self.root) while item: name = self.PatternTree.GetItemText(item) Names.append(name) if 'PWDR' in name: TextList.append([0.0,name]) DataList.append(self.PatternTree.GetItemPyData(item)[1]) # (x,y,w,yc,yb,yd) if not Inst: Inst = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,item, 'Instrument Parameters')) item, cookie = self.PatternTree.GetNextChild(self.root, cookie) if len(TextList) < 2: self.ErrorDialog('Not enough data to sum','There must be more than one "PWDR" pattern') return TextList.append('default_sum_name') dlg = self.SumDialog(self,'Sum data','Enter scale for each pattern in summation','PWDR',TextList) try: if dlg.ShowModal() == wx.ID_OK: lenX = 0 Xminmax = [0,0] Xsum = [] Ysum = [] Vsum = [] result = dlg.GetData() for i,item in enumerate(result[:-1]): scale,name = item data = DataList[i] if scale: Comments.append("%10.3f %s" % (scale,' * '+name)) x,y,w,yc,yb,yd = data #numpy arrays! v = 1./w if lenX: if lenX != len(x): self.ErrorDialog('Data length error','Data to be summed must have same number of points'+ \ '\nExpected:'+str(lenX)+ \ '\nFound: '+str(len(x))+'\nfor '+name) return else: lenX = len(x) if Xminmax[1]: if Xminmax != [x[0],x[-1]]: self.ErrorDialog('Data range error','Data to be summed must span same range'+ \ '\nExpected:'+str(Xminmax[0])+' '+str(Xminmax[1])+ \ '\nFound: '+str(x[0])+' '+str(x[-1])+'\nfor '+name) return else: for j,yi in enumerate(y): Ysum[j] += scale*yi Vsum[j] += abs(scale)*v[j] else: Xminmax = [x[0],x[-1]] YCsum = YBsum = YDsum = [0.0 for i in range(lenX)] for j,yi in enumerate(y): Xsum.append(x[j]) Ysum.append(scale*yi) Vsum.append(abs(scale*v[j])) Wsum = 1./np.array(Vsum) outname = 'PWDR '+result[-1] Id = 0 if outname in Names: dlg2 = wx.MessageDialog(self,'Overwrite data?','Duplicate data name',wx.OK|wx.CANCEL) try: if dlg2.ShowModal() == wx.ID_OK: Id = G2gd.GetPatternTreeItemId(self,self.root,name) self.PatternTree.Delete(Id) finally: dlg2.Destroy() Id = self.PatternTree.AppendItem(parent=self.root,text=outname) if Id: Sample = G2pdG.SetDefaultSample() valuesdict = { 'wtFactor':1.0, 'Dummy':False, 'ranId':ran.randint(0,sys.maxint), } self.PatternTree.SetItemPyData(Id,[valuesdict,[np.array(Xsum),np.array(Ysum),np.array(Wsum), np.array(YCsum),np.array(YBsum),np.array(YDsum)]]) self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),Comments) self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax]) self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',True,3,1.0,0.0,0.0], {'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}]) self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Instrument Parameters'),Inst) self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample) self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Peak List'),[]) self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Index Peak List'),[]) self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Unit Cells List'),[]) self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Reflection Lists'),{}) self.PatternTree.SelectItem(Id) self.PatternTree.Expand(Id) finally: dlg.Destroy() def OnImageSum(self,event): 'Sum together image data(?)' TextList = [] DataList = [] SumList = [] Names = [] Inst = [] SumItemList = [] Comments = ['Sum equals: \n'] if self.PatternTree.GetCount(): item, cookie = self.PatternTree.GetFirstChild(self.root) while item: name = self.PatternTree.GetItemText(item) Names.append(name) if 'IMG' in name: TextList.append([0.0,name]) DataList.append(self.PatternTree.GetItemPyData(item)) #Size,Image Data = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,item,'Image Controls')) item, cookie = self.PatternTree.GetNextChild(self.root, cookie) if len(TextList) < 2: self.ErrorDialog('Not enough data to sum','There must be more than one "IMG" pattern') return TextList.append('default_sum_name') dlg = self.SumDialog(self,'Sum data','Enter scale for each image in summation','IMG',TextList) try: if dlg.ShowModal() == wx.ID_OK: imSize = 0 result = dlg.GetData() First = True Found = False for i,item in enumerate(result[:-1]): scale,name = item data = DataList[i] if scale: Found = True Comments.append("%10.3f %s" % (scale,' * '+name)) Npix,imagefile = data image = G2IO.GetImageData(self,imagefile,imageOnly=True) if First: newImage = np.zeros_like(image) First = False if imSize: if imSize != Npix: self.ErrorDialog('Image size error','Images to be summed must be same size'+ \ '\nExpected:'+str(imSize)+ \ '\nFound: '+str(Npix)+'\nfor '+name) return newImage = newImage+scale*image else: imSize = Npix newImage = newImage+scale*image del(image) if not Found: self.ErrorDialog('Image sum error','No nonzero image multipliers found') return newImage = np.asfarray(newImage,dtype=np.float32) outname = 'IMG '+result[-1] Id = 0 if outname in Names: dlg2 = wx.MessageDialog(self,'Overwrite data?','Duplicate data name',wx.OK|wx.CANCEL) try: if dlg2.ShowModal() == wx.ID_OK: Id = G2gd.GetPatternTreeItemId(self,self.root,name) finally: dlg2.Destroy() else: Id = self.PatternTree.AppendItem(parent=self.root,text=outname) if Id: dlg = wx.FileDialog(self, 'Choose sum image filename', '.', '', 'G2img files (*.G2img)|*.G2img', wx.SAVE|wx.FD_OVERWRITE_PROMPT|wx.CHANGE_DIR) if dlg.ShowModal() == wx.ID_OK: newimagefile = dlg.GetPath() newimagefile = G2IO.FileDlgFixExt(dlg,newimagefile) G2IO.PutG2Image(newimagefile,Comments,Data,Npix,newImage) Imax = np.amax(newImage) Imin = np.amin(newImage) newImage = [] self.PatternTree.SetItemPyData(Id,[imSize,newimagefile]) self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),Comments) del(newImage) if self.imageDefault: Data = copy.copy(self.imageDefault) Data['showLines'] = True Data['ring'] = [] Data['rings'] = [] Data['cutoff'] = 10 Data['pixLimit'] = 20 Data['ellipses'] = [] Data['calibrant'] = '' Data['range'] = [(Imin,Imax),[Imin,Imax]] self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Image Controls'),Data) Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(Imin,Imax),[Imin,Imax]]} self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Masks'),Masks) self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Stress/Strain'),{}) self.PatternTree.SelectItem(Id) self.PatternTree.Expand(Id) self.PickId = G2gd.GetPatternTreeItemId(self,self.root,outname) self.Image = self.PickId finally: dlg.Destroy() def OnAddPhase(self,event): 'Add a new, empty phase to the tree. Called by Data/Add Phase menu' if not G2gd.GetPatternTreeItemId(self,self.root,'Phases'): sub = self.PatternTree.AppendItem(parent=self.root,text='Phases') else: sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases') PhaseName = '' dlg = wx.TextEntryDialog(None,'Enter a name for this phase','Phase Name Entry','New phase', style=wx.OK) if dlg.ShowModal() == wx.ID_OK: PhaseName = dlg.GetValue() dlg.Destroy() sub = self.PatternTree.AppendItem(parent=sub,text=PhaseName) E,SGData = G2spc.SpcGroup('P 1') self.PatternTree.SetItemPyData(sub,G2IO.SetNewPhase(Name=PhaseName,SGData=SGData)) def OnDeletePhase(self,event): 'Delete a phase from the tree. Called by Data/Delete Phase menu' #Hmm, also need to delete this phase from Reflection Lists for each PWDR histogram if self.dataFrame: self.dataFrame.Clear() TextList = [] DelList = [] DelItemList = [] if G2gd.GetPatternTreeItemId(self,self.root,'Phases'): sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases') else: return if sub: item, cookie = self.PatternTree.GetFirstChild(sub) while item: TextList.append(self.PatternTree.GetItemText(item)) item, cookie = self.PatternTree.GetNextChild(sub, cookie) dlg = wx.MultiChoiceDialog(self, 'Which phase to delete?', 'Delete phase', TextList, wx.CHOICEDLG_STYLE) try: if dlg.ShowModal() == wx.ID_OK: result = dlg.GetSelections() for i in result: DelList.append([i,TextList[i]]) item, cookie = self.PatternTree.GetFirstChild(sub) i = 0 while item: if [i,self.PatternTree.GetItemText(item)] in DelList: DelItemList.append(item) item, cookie = self.PatternTree.GetNextChild(sub, cookie) i += 1 for item in DelItemList: name = self.PatternTree.GetItemText(item) self.PatternTree.Delete(item) self.G2plotNB.Delete(name) item, cookie = self.PatternTree.GetFirstChild(self.root) while item: name = self.PatternTree.GetItemText(item) if 'PWDR' in name: Id = G2gd.GetPatternTreeItemId(self,item, 'Reflection Lists') refList = self.PatternTree.GetItemPyData(Id) for i,item in DelList: del(refList[item]) self.PatternTree.SetItemPyData(Id,refList) item, cookie = self.PatternTree.GetNextChild(self.root, cookie) finally: dlg.Destroy() def OnRenameData(self,event): 'Renames an existing phase. Called by Data/Rename Phase menu' name = self.PatternTree.GetItemText(self.PickId) if 'PWDR' in name or 'HKLF' in name or 'IMG' in name: dataType = name[:name.index(' ')+1] #includes the ' ' dlg = wx.TextEntryDialog(self,'Data name: '+dataType,'Change data name', defaultValue=name[name.index(' ')+1:]) try: if dlg.ShowModal() == wx.ID_OK: self.PatternTree.SetItemText(self.PickId,dataType+dlg.GetValue()) finally: dlg.Destroy() def GetFileList(self,fileType,skip=None): #potentially useful? 'Appears unused. Note routine of same name in GSASIIpwdGUI' fileList = [] Source = '' id, cookie = self.PatternTree.GetFirstChild(self.root) while id: name = self.PatternTree.GetItemText(id) if fileType in name: if id == skip: Source = name else: fileList.append([False,name,id]) id, cookie = self.PatternTree.GetNextChild(self.root, cookie) if skip: return fileList,Source else: return fileList def OnDataDelete(self, event): '''Delete one or more histograms from data tree. Called by the Data/DeleteData menu ''' TextList = ['All Data'] DelList = [] DelItemList = [] ifPWDR = False ifIMG = False ifHKLF = False ifPDF = False if self.PatternTree.GetCount(): item, cookie = self.PatternTree.GetFirstChild(self.root) while item: name = self.PatternTree.GetItemText(item) if name not in ['Notebook','Controls','Covariance','Constraints','Restraints','Phases']: if 'PWDR' in name: ifPWDR = True if 'IMG' in name: ifIMG = True if 'HKLF' in name: ifHKLF = True if 'PDF' in name: ifPDF = True TextList.append(name) item, cookie = self.PatternTree.GetNextChild(self.root, cookie) if ifPWDR: TextList.insert(1,'All PWDR') if ifIMG: TextList.insert(1,'All IMG') if ifHKLF: TextList.insert(1,'All HKLF') if ifPDF: TextList.insert(1,'All PDF') dlg = wx.MultiChoiceDialog(self, 'Which data to delete?', 'Delete data', TextList, wx.CHOICEDLG_STYLE) try: if dlg.ShowModal() == wx.ID_OK: result = dlg.GetSelections() for i in result: DelList.append(TextList[i]) if 'All Data' in DelList: DelList = [item for item in TextList if item[:3] != 'All'] elif 'All PWDR' in DelList: DelList = [item for item in TextList if item[:4] == 'PWDR'] elif 'All IMG' in DelList: DelList = [item for item in TextList if item[:3] == 'IMG'] elif 'All HKLF' in DelList: DelList = [item for item in TextList if item[:4] == 'HKLF'] elif 'All PDF' in DelList: DelList = [item for item in TextList if item[:3] == 'PDF'] item, cookie = self.PatternTree.GetFirstChild(self.root) while item: if self.PatternTree.GetItemText(item) in DelList: DelItemList.append(item) item, cookie = self.PatternTree.GetNextChild(self.root, cookie) for item in DelItemList: self.PatternTree.Delete(item) self.PickId = 0 wx.CallAfter(G2plt.PlotPatterns,self,True) #so plot gets updated finally: dlg.Destroy() def OnFileOpen(self, event, filename=None): '''Reads in a GSAS-II .gpx project file in response to the File/Open Project menu button ''' result = wx.ID_OK Id = 0 if self.PatternTree.GetChildrenCount(self.root,False): if self.dataFrame: self.dataFrame.Clear() dlg = wx.MessageDialog( self, 'Do you want to overwrite the current project? ' 'Any unsaved changes will be lost. Press OK to continue.', 'Overwrite?', wx.OK | wx.CANCEL) try: result = dlg.ShowModal() if result == wx.ID_OK: self.PatternTree.DeleteChildren(self.root) self.GSASprojectfile = '' if self.HKL: self.HKL = [] if self.G2plotNB.plotList: self.G2plotNB.clear() finally: dlg.Destroy() if result != wx.ID_OK: return if not filename: if self.dataDisplay: self.dataDisplay.Destroy() dlg = wx.FileDialog(self, 'Choose GSAS-II project file', '.', '', 'GSAS-II project file (*.gpx)|*.gpx',wx.OPEN|wx.CHANGE_DIR) try: if dlg.ShowModal() != wx.ID_OK: return self.GSASprojectfile = dlg.GetPath() self.GSASprojectfile = G2IO.FileDlgFixExt(dlg,self.GSASprojectfile) self.dirname = dlg.GetDirectory() finally: dlg.Destroy() else: self.GSASprojectfile = os.path.splitext(filename)[0]+'.gpx' self.dirname = os.path.split(filename)[0] G2IO.ProjFileOpen(self) self.PatternTree.SetItemText(self.root,'Loaded Data: '+self.GSASprojectfile) self.PatternTree.Expand(self.root) self.HKL = [] item, cookie = self.PatternTree.GetFirstChild(self.root) while item and not Id: name = self.PatternTree.GetItemText(item) if name[:4] in ['PWDR','HKLF','IMG ','PDF ']: Id = item elif name == 'Controls': data = self.PatternTree.GetItemPyData(item) if data: for item in self.Refine: item.Enable(True) for item in self.SeqRefine: item.Enable(True) item, cookie = self.PatternTree.GetNextChild(self.root, cookie) if Id: self.PatternTree.SelectItem(Id) self.CheckNotebook() os.chdir(self.dirname) # to get Mac/Linux to change directory! def OnFileClose(self, event): '''Clears the data tree in response to the File/New Project menu button. User is given option to save the project. ''' if self.dataFrame: self.dataFrame.Clear() self.dataFrame.SetLabel('GSAS-II data display') dlg = wx.MessageDialog(self, 'Save current project?', ' ', wx.YES | wx.NO | wx.CANCEL) try: result = dlg.ShowModal() if result == wx.ID_OK: self.OnFileSaveMenu(event) if result != wx.ID_CANCEL: self.GSASprojectfile = '' self.PatternTree.SetItemText(self.root,'Loaded Data: ') self.PatternTree.DeleteChildren(self.root) if self.HKL: self.HKL = [] if self.G2plotNB.plotList: self.G2plotNB.clear() finally: dlg.Destroy() def OnFileSave(self, event): '''Save the current project in response to the File/Save Project menu button ''' if self.GSASprojectfile: self.PatternTree.SetItemText(self.root,'Loaded Data: '+self.GSASprojectfile) G2IO.ProjFileSave(self) else: self.OnFileSaveas(event) def OnFileSaveas(self, event): '''Save the current project in response to the File/Save as menu button ''' dlg = wx.FileDialog(self, 'Choose GSAS-II project file name', '.', '', 'GSAS-II project file (*.gpx)|*.gpx',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT|wx.CHANGE_DIR) try: if dlg.ShowModal() == wx.ID_OK: self.GSASprojectfile = dlg.GetPath() self.GSASprojectfile = G2IO.FileDlgFixExt(dlg,self.GSASprojectfile) self.PatternTree.SetItemText(self.root,'Saving project as'+self.GSASprojectfile) self.SetTitle("GSAS-II data tree: "+os.path.split(self.GSASprojectfile)[1]) G2IO.ProjFileSave(self) os.chdir(dlg.GetDirectory()) # to get Mac/Linux to change directory! finally: dlg.Destroy() def ExitMain(self, event): '''Called if the main window is closed''' if self.undofile: os.remove(self.undofile) sys.exit() def OnFileExit(self, event): '''Called in response to the File/Quit menu button''' if self.dataFrame: self.dataFrame.Clear() self.dataFrame.Destroy() self.Close() def OnExportPatterns(self,event): names = ['All'] exports = [] item, cookie = self.PatternTree.GetFirstChild(self.root) while item: name = self.PatternTree.GetItemText(item) if 'PWDR' in name: names.append(name) item, cookie = self.PatternTree.GetNextChild(self.root, cookie) if names: dlg = wx.MultiChoiceDialog(self,'Select','Powder patterns to export',names) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelections() if sel[0] == 0: exports = names[1:] else: for x in sel: exports.append(names[x]) dlg.Destroy() if exports: dlg = wx.FileDialog(self, 'Choose output powder file name', '.', '', 'GSAS fxye file (*.fxye)|*.fxye|xye file (*.xye)|*.xye', wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT|wx.CHANGE_DIR) try: if dlg.ShowModal() == wx.ID_OK: powderfile = dlg.GetPath() powderfile = G2IO.FileDlgFixExt(dlg,powderfile) if 'fxye' in powderfile: G2IO.powderFxyeSave(self,exports,powderfile) else: #just xye G2IO.powderXyeSave(self,exports,powderfile) finally: dlg.Destroy() def OnExportPeakList(self,event): dlg = wx.FileDialog(self, 'Choose output peak list file name', '.', '', '(*.*)|*.*',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT|wx.CHANGE_DIR) try: if dlg.ShowModal() == wx.ID_OK: self.peaklistfile = dlg.GetPath() self.peaklistfile = G2IO.FileDlgFixExt(dlg,self.peaklistfile) file = open(self.peaklistfile,'w') item, cookie = self.PatternTree.GetFirstChild(self.root) while item: name = self.PatternTree.GetItemText(item) if 'PWDR' in name: item2, cookie2 = self.PatternTree.GetFirstChild(item) while item2: name2 = self.PatternTree.GetItemText(item2) if name2 == 'Peak List': peaks = self.PatternTree.GetItemPyData(item2) file.write("%s \n" % (name+' Peak List')) for peak in peaks: file.write("%10.5f %12.2f %10.3f %10.3f \n" % \ (peak[0],peak[2],peak[4],peak[6])) item2, cookie2 = self.PatternTree.GetNextChild(item, cookie2) item, cookie = self.PatternTree.GetNextChild(self.root, cookie) file.close() finally: dlg.Destroy() def OnExportHKL(self,event): dlg = wx.FileDialog(self, 'Choose output reflection list file name', '.', '', '(*.*)|*.*',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT|wx.CHANGE_DIR) try: if dlg.ShowModal() == wx.ID_OK: self.peaklistfile = dlg.GetPath() self.peaklistfile = G2IO.FileDlgFixExt(dlg,self.peaklistfile) file = open(self.peaklistfile,'w') item, cookie = self.PatternTree.GetFirstChild(self.root) while item: name = self.PatternTree.GetItemText(item) if 'PWDR' in name: item2, cookie2 = self.PatternTree.GetFirstChild(item) while item2: name2 = self.PatternTree.GetItemText(item2) if name2 == 'Reflection Lists': data = self.PatternTree.GetItemPyData(item2) phases = data.keys() for phase in phases: peaks = data[phase] file.write("%s %s %s \n" % (name,phase,' Reflection List')) file.write('%s \n'%(' h k l m d-space 2-theta wid F**2')) for peak in peaks: FWHM = G2pwd.getgamFW(peak[7],peak[6])/50. #to get delta-2-theta in deg. file.write(" %3d %3d %3d %3d %10.5f %10.5f %10.5f %10.3f \n" % \ (int(peak[0]),int(peak[1]),int(peak[2]),int(peak[3]),peak[4],peak[5],FWHM,peak[8])) item2, cookie2 = self.PatternTree.GetNextChild(item, cookie2) item, cookie = self.PatternTree.GetNextChild(self.root, cookie) file.close() finally: dlg.Destroy() def OnExportPDF(self,event): #need S(Q) and G(R) to be saved here - probably best from selection? names = ['All'] exports = [] item, cookie = self.PatternTree.GetFirstChild(self.root) while item: name = self.PatternTree.GetItemText(item) if 'PDF' in name: names.append(name) item, cookie = self.PatternTree.GetNextChild(self.root, cookie) if names: dlg = wx.MultiChoiceDialog(self,'Select','PDF patterns to export',names) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelections() if sel[0] == 0: exports = names[1:] else: for x in sel: exports.append(names[x]) dlg.Destroy() if exports: G2IO.PDFSave(self,exports) def OnMakePDFs(self,event): '''Calculates PDFs ''' tth2q = lambda t,w:4.0*math.pi*sind(t/2.0)/w TextList = ['All PWDR'] PDFlist = [] Names = [] if self.PatternTree.GetCount(): id, cookie = self.PatternTree.GetFirstChild(self.root) while id: name = self.PatternTree.GetItemText(id) Names.append(name) if 'PWDR' in name: TextList.append(name) id, cookie = self.PatternTree.GetNextChild(self.root, cookie) if len(TextList) == 1: self.ErrorDialog('Nothing to make PDFs for','There must be at least one "PWDR" pattern') return dlg = wx.MultiChoiceDialog(self,'Make PDF controls','Make PDF controls for:',TextList, wx.CHOICEDLG_STYLE) try: if dlg.ShowModal() == wx.ID_OK: result = dlg.GetSelections() for i in result: PDFlist.append(TextList[i]) if 0 in result: PDFlist = [item for item in TextList if item[:4] == 'PWDR'] for item in PDFlist: PWDRname = item[4:] Id = self.PatternTree.AppendItem(parent=self.root,text='PDF '+PWDRname) Data = { 'Sample':{'Name':item,'Mult':1.0,'Add':0.0}, 'Sample Bkg.':{'Name':'','Mult':-1.0,'Add':0.0}, 'Container':{'Name':'','Mult':-1.0,'Add':0.0}, 'Container Bkg.':{'Name':'','Mult':-1.0,'Add':0.0},'ElList':{}, 'Geometry':'Cylinder','Diam':1.0,'Pack':0.50,'Form Vol':10.0, 'DetType':'Image plate','ObliqCoeff':0.2,'Ruland':0.025,'QScaleLim':[0,100], 'Lorch':True,} self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='PDF Controls'),Data) self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='I(Q)'+PWDRname),[]) self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='S(Q)'+PWDRname),[]) self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='F(Q)'+PWDRname),[]) self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='G(R)'+PWDRname),[]) for item in self.ExportPDF: item.Enable(True) finally: dlg.Destroy() def GetPWDRdatafromTree(self,PWDRname): ''' Returns powder data from GSASII tree :param str PWDRname: a powder histogram name as obtained from :meth:`GSASIIstruct.GetHistogramNames` :returns: PWDRdata = powder data dictionary with Powder data arrays, Limits, Instrument Parameters, Sample Parameters ''' PWDRdata = {} try: PWDRdata.update(self.PatternTree.GetItemPyData(PWDRname)[0]) #wtFactor + ? except ValueError: PWDRdata['wtFactor'] = 1.0 PWDRdata['Data'] = self.PatternTree.GetItemPyData(PWDRname)[1] #powder data arrays PWDRdata['Limits'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Limits')) PWDRdata['Background'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Background')) PWDRdata['Instrument Parameters'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Instrument Parameters')) PWDRdata['Sample Parameters'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Sample Parameters')) PWDRdata['Reflection Lists'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,PWDRname,'Reflection Lists')) if 'ranId' not in PWDRdata: # patch, add a random Id PWDRdata['ranId'] = ran.randint(0,sys.maxint) if 'ranId' not in PWDRdata['Sample Parameters']: # I hope this becomes obsolete at some point PWDRdata['Sample Parameters']['ranId'] = PWDRdata['ranId'] return PWDRdata def GetHKLFdatafromTree(self,HKLFname): ''' Returns single crystal data from GSASII tree :param str HKLFname: a single crystal histogram name as obtained from :meth:`GSASIIstruct.GetHistogramNames` :returns: HKLFdata = single crystal data list of reflections ''' HKLFdata = {} HKLFdata.update(self.PatternTree.GetItemPyData(HKLFname)[0]) #wtFactor + ? # try: # HKLFdata.update(self.PatternTree.GetItemPyData(HKLFname)[0]) #wtFactor + ? # except ValueError: # HKLFdata['wtFactor'] = 1.0 HKLFdata['Data'] = self.PatternTree.GetItemPyData(HKLFname)[1] HKLFdata['Instrument Parameters'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,HKLFname,'Instrument Parameters')) return HKLFdata def GetPhaseData(self): '''Returns a dict with defined phases. Note routine :func:`GSASIIstrIO.GetPhaseData` also exists to get same info from GPX file. ''' phaseData = {} if G2gd.GetPatternTreeItemId(self,self.root,'Phases'): sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases') else: print 'no phases found in GetPhaseData' sub = None if sub: item, cookie = self.PatternTree.GetFirstChild(sub) while item: phaseName = self.PatternTree.GetItemText(item) phaseData[phaseName] = self.PatternTree.GetItemPyData(item) if 'ranId' not in phaseData[phaseName]: phaseData[phaseName]['ranId'] = ran.randint(0,sys.maxint) item, cookie = self.PatternTree.GetNextChild(sub, cookie) return phaseData def GetPhaseNames(self): '''Returns a list of defined phases. Note routine :func:`GSASIIstrIO.GetPhaseNames` also exists to get same info from GPX file. ''' phaseNames = [] if G2gd.GetPatternTreeItemId(self,self.root,'Phases'): sub = G2gd.GetPatternTreeItemId(self,self.root,'Phases') else: print 'no phases found in GetPhaseNames' sub = None if sub: item, cookie = self.PatternTree.GetFirstChild(sub) while item: phase = self.PatternTree.GetItemText(item) phaseNames.append(phase) item, cookie = self.PatternTree.GetNextChild(sub, cookie) return phaseNames def GetHistogramNames(self,hType): """ Returns a list of histogram names found in the GSASII data tree Note routine :func:`GSASIIstrIO.GetHistogramNames` also exists to get same info from GPX file. :param str hType: list of histogram types :return: list of histogram names """ HistogramNames = [] if self.PatternTree.GetCount(): item, cookie = self.PatternTree.GetFirstChild(self.root) while item: name = self.PatternTree.GetItemText(item) if name[:4] in hType: HistogramNames.append(name) item, cookie = self.PatternTree.GetNextChild(self.root, cookie) return HistogramNames def GetUsedHistogramsAndPhasesfromTree(self): ''' Returns all histograms that are found in any phase and any phase that uses a histogram. This also assigns numbers to used phases and histograms by the order they appear in the file. Note routine :func:`GSASIIstrIO.GetUsedHistogramsAndPhasesfromTree` also exists to get same info from GPX file. :returns: (Histograms,Phases) * Histograms = dictionary of histograms as {name:data,...} * Phases = dictionary of phases that use histograms ''' Histograms = {} Phases = {} phaseNames = self.GetPhaseNames() phaseData = self.GetPhaseData() histoList = self.GetHistogramNames(['PWDR','HKLF']) for phase in phaseData: Phase = phaseData[phase] pId = phaseNames.index(phase) Phase['pId'] = pId if Phase['Histograms']: if phase not in Phases: Phases[phase] = Phase for hist in Phase['Histograms']: if 'Use' not in Phase['Histograms'][hist]: #patch: add Use flag as True Phase['Histograms'][hist]['Use'] = True if hist not in Histograms and Phase['Histograms'][hist]['Use']: item = G2gd.GetPatternTreeItemId(self,self.root,hist) if item: if 'PWDR' in hist[:4]: Histograms[hist] = self.GetPWDRdatafromTree(item) elif 'HKLF' in hist[:4]: Histograms[hist] = self.GetHKLFdatafromTree(item) hId = histoList.index(hist) Histograms[hist]['hId'] = hId else: # would happen if a referenced histogram were renamed or deleted print('For phase "'+str(phase)+ '" unresolved reference to histogram "'+str(hist)+'"') #G2obj.IndexAllIds(Histograms=Histograms,Phases=Phases) G2obj.IndexAllIds(Histograms=Histograms,Phases=phaseData) return Histograms,Phases def MakeLSParmDict(self): '''Load all parameters used for computation from the tree into a dict :returns: (parmDict,varyList) where: * parmDict is a dict with values and refinement flags for each parameter and * varyList is a list of variables (refined parameters). ''' parmDict = {} Histograms,Phases = self.GetUsedHistogramsAndPhasesfromTree() for phase in Phases: if 'pId' not in Phases[phase]: self.ErrorDialog('View parameter error','You must run least squares at least once') raise Exception,'No pId for phase '+str(phase) rigidbodyDict = self.PatternTree.GetItemPyData( G2gd.GetPatternTreeItemId(self,self.root,'Rigid bodies')) rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False) rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]}) Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtable,BLtable = G2stIO.GetPhaseData(Phases,RestraintDict=None,rbIds=rbIds,Print=False) hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(Phases,Histograms,Print=False) histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False) varyList = rbVary+phaseVary+hapVary+histVary parmDict.update(rbDict) parmDict.update(phaseDict) parmDict.update(hapDict) parmDict.update(histDict) for parm in parmDict: if parm.split(':')[-1] in ['Azimuth','Gonio. radius','Lam1','Lam2', 'Omega','Chi','Phi','nDebye','nPeaks']: parmDict[parm] = [parmDict[parm],'-'] elif parm.split(':')[-2] in ['Ax','Ay','Az','SHmodel','SHord']: parmDict[parm] = [parmDict[parm],'-'] elif parm in varyList: parmDict[parm] = [parmDict[parm],'T'] else: parmDict[parm] = [parmDict[parm],'F'] return parmDict,varyList def ShowLSParms(self,event): '''Displays a window showing all parameters in the refinement. Called from the Calculate/View LS Parms menu. ''' parmDict,varyList = self.MakeLSParmDict() dlg = G2gd.ShowLSParms(self,'Least Squares Parameters',parmDict,varyList) dlg.ShowModal() dlg.Destroy() def OnRefine(self,event): '''Perform a refinement. Called from the Calculate/Refine menu. ''' self.OnFileSave(event) # check that constraints are OK here errmsg, warnmsg = G2stIO.CheckConstraints(self.GSASprojectfile) if errmsg: print('Error in constraints:\n'+errmsg+ '\nRefinement not possible') self.ErrorDialog('Constraint Error', 'Error in constraints:\n'+errmsg+ '\nRefinement not possible') return if warnmsg: print('Conflict between refinment flag settings and constraints:\n'+ warnmsg+'\nRefinement not possible') self.ErrorDialog('Refinement Flag Error', 'Conflict between refinment flag settings and constraints:\n'+ warnmsg+ '\nRefinement not possible') return #works - but it'd be better if it could restore plots dlg = wx.ProgressDialog('Residual','All data Rw =',101.0, style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT) screenSize = wx.ClientDisplayRect() Size = dlg.GetSize() Size = (int(Size[0]*1.2),Size[1]) # increase size a bit along x dlg.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5)) dlg.SetSize(Size) Rw = 100.00 try: Rw = G2stMn.Refine(self.GSASprojectfile,dlg) finally: dlg.Destroy() oldId = self.PatternTree.GetSelection() oldName = self.PatternTree.GetItemText(oldId) parentId = self.PatternTree.GetItemParent(oldId) parentName = '' if parentId: parentName = self.PatternTree.GetItemText(parentId) dlg = wx.MessageDialog(self,'Load new result?','Refinement results, Rw =%.3f'%(Rw),wx.OK|wx.CANCEL) try: if dlg.ShowModal() == wx.ID_OK: Id = 0 self.PatternTree.DeleteChildren(self.root) if self.HKL: self.HKL = [] if self.G2plotNB.plotList: self.G2plotNB.clear() G2IO.ProjFileOpen(self) item, cookie = self.PatternTree.GetFirstChild(self.root) while item and not Id: name = self.PatternTree.GetItemText(item) if name[:4] in ['PWDR','HKLF']: Id = item item, cookie = self.PatternTree.GetNextChild(self.root, cookie) if parentName: parentId = G2gd.GetPatternTreeItemId(self, self.root, parentName) if parentId: itemId = G2gd.GetPatternTreeItemId(self, parentId, oldName) else: itemId = G2gd.GetPatternTreeItemId(self, self.root, oldName) self.PatternTree.SelectItem(itemId) elif Id: self.PatternTree.SelectItem(Id) finally: dlg.Destroy() def OnSeqRefine(self,event): '''Perform a sequential refinement. Called from the Calculate/Sequential refine menu. ''' Id = G2gd.GetPatternTreeItemId(self,self.root,'Sequential results') if not Id: Id = self.PatternTree.AppendItem(self.root,text='Sequential results') self.PatternTree.SetItemPyData(Id,{}) self.OnFileSave(event) # check that constraints are OK here errmsg, warnmsg = G2stIO.CheckConstraints(self.GSASprojectfile) if errmsg: print('Error in constraints:\n'+errmsg+ '\nRefinement not possible') self.ErrorDialog('Constraint Error', 'Error in constraints:\n'+errmsg+ '\nRefinement not possible') return if warnmsg: print('Conflict between refinment flag settings and constraints:\n'+ warnmsg+'\nRefinement not possible') self.ErrorDialog('Refinement Flag Error', 'Conflict between refinment flag settings and constraints:\n'+ warnmsg+'\nRefinement not possible') return dlg = wx.ProgressDialog('Residual for histogram 0','Powder profile Rwp =',101.0, style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT) screenSize = wx.ClientDisplayRect() Size = dlg.GetSize() Size = (int(Size[0]*1.2),Size[1]) # increase size a bit along x dlg.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5)) dlg.SetSize(Size) try: G2stMn.SeqRefine(self.GSASprojectfile,dlg) finally: dlg.Destroy() dlg = wx.MessageDialog(self,'Load new result?','Refinement results',wx.OK|wx.CANCEL) try: if dlg.ShowModal() == wx.ID_OK: Id = 0 self.PatternTree.DeleteChildren(self.root) if self.HKL: self.HKL = [] if self.G2plotNB.plotList: self.G2plotNB.clear() G2IO.ProjFileOpen(self) item, cookie = self.PatternTree.GetFirstChild(self.root) while item and not Id: name = self.PatternTree.GetItemText(item) if name[:4] in ['PWDR','HKLF']: Id = item item, cookie = self.PatternTree.GetNextChild(self.root, cookie) if Id: self.PatternTree.SelectItem(Id) finally: dlg.Destroy() def ErrorDialog(self,title,message,parent=None, wtype=wx.OK): 'Display an error message' result = None if parent is None: dlg = wx.MessageDialog(self, message, title, wtype) else: dlg = wx.MessageDialog(parent, message, title, wtype) dlg.CenterOnParent() # not working on Mac try: result = dlg.ShowModal() finally: dlg.Destroy() return result class GSASIImain(wx.App): '''Defines a wxApp for GSAS-II Creates a wx frame (self.main) which contains the display of the data tree. ''' def OnInit(self): '''Called automatically when the app is created.''' self.main = GSASII(None) self.main.Show() self.SetTopWindow(self.main) return True def MacOpenFile(self, filename): '''Called on Mac every time a file is dropped on the app when it is running, treat this like a File/Open project menu action. Should be ignored on other platforms ''' self.main.OnFileOpen(None,filename) def main(): '''Start up the GSAS-II application''' #application = GSASIImain() # don't redirect output, someday we # may want to do this if we can application = GSASIImain(0) if wxInspector: import wx.lib.inspection as wxeye wxeye.InspectionTool().Show() #application.main.OnRefine(None) application.MainLoop() if __name__ == '__main__': main() # start the GUI