Changeset 3000 for trunk/GSASIIscriptable.py

Timestamp:

Aug 11, 2017 5:34:54 PM (5 years ago)

Author:

toby

Message:

make the two frame version the trunk as we hit version 3000

Location:

trunk

Files:

• . (modified) (1 prop)
• GSASIIscriptable.py (modified) (5 diffs)

trunk/GSASIIscriptable.py

@@ +1 @@
+#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 ########### SVN repository information ###################
@@ -8 +9 @@
 ########### SVN repository information ###################
 """
-
+*GSASIIscriptable: Scripting Tools*
+-----------------------------------
+
+Routines for reading, writing, modifying and creating GSAS-II project (.gpx) files.
+
+Supports a command line interface as well.
 """
+from __future__ import division, print_function # needed?
 import os.path as ospath
 import sys
@@ -15 +22 @@
 import imp
 import copy
+import platform
+import os
+import random as ran
+import json
+
+import numpy.ma as ma
+import scipy.interpolate as si
+import numpy as np
+import scipy as sp
+import matplotlib as mpl
+
 import GSASIIpath
+GSASIIpath.SetBinaryPath(False) # would rather have this in __name__ == '__main__' stanza
+import GSASIIIO as G2IO
+import GSASIIfiles as G2fil
 import GSASIIobj as G2obj
+import GSASIIpwd as G2pwd
+import GSASIIstrIO as G2strIO
+import GSASIIspc as G2spc
+import GSASIIstrMain as G2strMain
+import GSASIImath as G2mth
+import GSASIIElem as G2elem
+
+try:
+    import matplotlib.pyplot as plt
+except ImportError:
+    plt = None
 
 def LoadDictFromProjFile(ProjFile):
-    ''''Read a GSAS-II project file and load items to dictionary
-    :param: str ProjFile: GSAS-II project (name.gpx) full file name
-    :returns: dict Project: representation of gpx file following the GSAS-II tree struture
+    '''Read a GSAS-II project file and load items to dictionary
+    :param str ProjFile: GSAS-II project (name.gpx) full file name
+    :returns: Project,nameList, where
+
+      * Project (dict) is a representation of gpx file following the GSAS-II tree struture
         for each item: key = tree name (e.g. 'Controls','Restraints',etc.), data is dict
         data dict = {'data':item data whch may be list, dict or None,'subitems':subdata (if any)}
-    :returns: list nameList: names of main tree entries & subentries used to reconstruct project file
-    Example for fap.gpx:
-    Project = {                 #NB:dict order is not tree order
-        u'Phases':{'data':None,'fap':{phase dict}}, 
-        u'PWDR FAP.XRA Bank 1':{'data':[histogram data list],'Comments':comments,'Limits':limits, etc}, 
+      * nameList (list) has names of main tree entries & subentries used to reconstruct project file
+
+    Example for fap.gpx::
+
+      Project = {                 #NB:dict order is not tree order
+        u'Phases':{'data':None,'fap':{phase dict}},
+        u'PWDR FAP.XRA Bank 1':{'data':[histogram data list],'Comments':comments,'Limits':limits, etc},
         u'Rigid bodies':{'data': {rigid body dict}},
         u'Covariance':{'data':{covariance data dict}},
-        u'Controls':{'data':{controls data dict}}, 
-        u'Notebook':{'data':[notebook list]}, 
-        u'Restraints':{'data':{restraint data dict}}, 
-        u'Constraints':{'data':{constraint data dict}}]}
-    nameList = [                #NB: reproduces tree order
+        u'Controls':{'data':{controls data dict}},
+        u'Notebook':{'data':[notebook list]},
+        u'Restraints':{'data':{restraint data dict}},
+        u'Constraints':{'data':{constraint data dict}}]
+        }
+      nameList = [                #NB: reproduces tree order
         [u'Notebook',],
-        [u'Controls',], 
-        [u'Covariance',], 
+        [u'Controls',],
+        [u'Covariance',],
         [u'Constraints',],
-        [u'Restraints',], 
-        [u'Rigid bodies',], 
+        [u'Restraints',],
+        [u'Rigid bodies',],
         [u'PWDR FAP.XRA Bank 1',
-             u'Comments', 
-             u'Limits', 
-             u'Background', 
+             u'Comments',
+             u'Limits',
+             u'Background',
              u'Instrument Parameters',
-             u'Sample Parameters', 
-             u'Peak List', 
-             u'Index Peak List', 
-             u'Unit Cells List', 
-             u'Reflection Lists'], 
-        [u'Phases', 
-             u'fap']]
+             u'Sample Parameters',
+             u'Peak List',
+             u'Index Peak List',
+             u'Unit Cells List',
+             u'Reflection Lists'],
+        [u'Phases', u'fap']
+        ]
     '''
-    if not ospath.exists(ProjFile):
-        print ('\n*** Error attempt to open project file that does not exist:\n   '+
-            str(ProjFile))
-        return
+    # Let IOError be thrown if file does not exist
+    # if not ospath.exists(ProjFile):
+    #     print ('\n*** Error attempt to open project file that does not exist:\n   '+
+    #         str(ProjFile))
+    #     return
     file = open(ProjFile,'rb')
-    print 'loading from file: ',ProjFile
+    # print('loading from file: {}'.format(ProjFile))
     Project = {}
     nameList = []
@@ -76 +114 @@
                 nameList[-1].append(datus[0])
         file.close()
-        print('project load successful')
+        # print('project load successful')
     except:
-        print("Error reading file "+str(ProjFile)+". This is not a GSAS-II .gpx file")
-        return None
+        raise IOError("Error reading file "+str(ProjFile)+". This is not a GSAS-II .gpx file")
+    finally:
+        file.close()
     return Project,nameList
-    
+
 def SaveDictToProjFile(Project,nameList,ProjFile):
     '''Save a GSAS-II project file from dictionary/nameList created by LoadDictFromProjFile
-    param: dict Project: representation of gpx file following the GSAS-II 
-        tree struture as described for LoadDictFromProjFile
-    param: list nameList: names of main tree entries & subentries used to reconstruct project file
-    param: str ProjFile: full file name for output project.gpx file (including extension)
+
+    :param dict Project: representation of gpx file following the GSAS-II
+      tree structure as described for LoadDictFromProjFile
+    :param list nameList: names of main tree entries & subentries used to reconstruct project file
+    :param str ProjFile: full file name for output project.gpx file (including extension)
     '''
     file = open(ProjFile,'wb')
-    print 'save to file: ',ProjFile
-    for name in nameList:
-        data = []
-        item = Project[name[0]]
-        data.append([name[0],item['data']])
-        for item2 in name[1:]:
-            data.append([item2,item[item2]])
-        cPickle.dump(data,file,1)
-    file.close()
-    print('project save successful')
-    
+    # print('save to file: {}'.format(ProjFile))
+    try:
+        for name in nameList:
+            data = []
+            item = Project[name[0]]
+            data.append([name[0],item['data']])
+            for item2 in name[1:]:
+                data.append([item2,item[item2]])
+            cPickle.dump(data,file,1)
+    finally:
+        file.close()
+    # print('project save successful')
+
 def ImportPowder(reader,filename):
     '''Use a reader to import a powder diffraction data file
-    param: str reader: a scriptable reader
-    param: str filename: full name of powder data file; can be "multi-Bank" data
-    returns: list rdlist: list of rrader objects containing powder data, one for each
-        "Bank" of data encountered in file
-        items in reader object of interest are:
-            rd.comments: list of str: comments found on powder file
-            rd.dnames: list of str: data nammes suitable for use in GSASII data tree
-                NB: duplicated in all rd entries in rdlist
-            rd.powderdata: list of numpy arrays: pos,int,wt,zeros,zeros,zeros as needed 
-                for a PWDR entry in  GSASII data tree.        
+
+    :param str reader: a scriptable reader
+    :param str filename: full name of powder data file; can be "multi-Bank" data
+
+    :returns list rdlist: list of reader objects containing powder data, one for each
+      "Bank" of data encountered in file. Items in reader object of interest are:
+
+        * rd.comments: list of str: comments found on powder file
+        * rd.dnames: list of str: data nammes suitable for use in GSASII data tree NB: duplicated in all rd entries in rdlist
+        * rd.powderdata: list of numpy arrays: pos,int,wt,zeros,zeros,zeros as needed for a PWDR entry in  GSASII data tree.
     '''
     rdfile,rdpath,descr = imp.find_module(reader)
     rdclass = imp.load_module(reader,rdfile,rdpath,descr)
-    rd = rdclass.GSAS_ReaderClass()    
+    rd = rdclass.GSAS_ReaderClass()
     if not rd.scriptable:
-        print '**** ERROR: ',reader,' is not a scriptable reader'
+        print(u'**** ERROR: '+reader+u' is not a scriptable reader')
         return None
     fl = open(filename,'rb')
@@ -137 +179 @@
                     repeat = True
         return rdlist
-    print rd.errors
+    print(rd.errors)
     return None
-    
+
+def SetDefaultDData(dType,histoName,NShkl=0,NDij=0):
+    '''Create an initial Histogram dictionary
+
+    Author: Jackson O'Donnell jacksonhodonnell@gmail.com
+    '''
+    if dType in ['SXC','SNC']:
+        return {'Histogram':histoName,'Show':False,'Scale':[1.0,True],
+            'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]},
+            'Extinction':['Lorentzian','None', {'Tbar':0.1,'Cos2TM':0.955,
+            'Eg':[1.e-10,False],'Es':[1.e-10,False],'Ep':[1.e-10,False]}],
+            'Flack':[0.0,False]}
+    elif dType == 'SNT':
+        return {'Histogram':histoName,'Show':False,'Scale':[1.0,True],
+            'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]},
+            'Extinction':['Lorentzian','None', {
+            'Eg':[1.e-10,False],'Es':[1.e-10,False],'Ep':[1.e-10,False]}]}
+    elif 'P' in dType:
+        return {'Histogram':histoName,'Show':False,'Scale':[1.0,False],
+            'Pref.Ori.':['MD',1.0,False,[0,0,1],0,{},[],0.1],
+            'Size':['isotropic',[1.,1.,1.],[False,False,False],[0,0,1],
+                [1.,1.,1.,0.,0.,0.],6*[False,]],
+            'Mustrain':['isotropic',[1000.0,1000.0,1.0],[False,False,False],[0,0,1],
+                NShkl*[0.01,],NShkl*[False,]],
+            'HStrain':[NDij*[0.0,],NDij*[False,]],
+            'Extinction':[0.0,False],'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]}}
+
+
+def PreSetup(data):
+    '''Create part of an initial (empty) phase dictionary
+
+    from GSASIIphsGUI.py, near end of UpdatePhaseData
+    Author: Jackson O'Donnell jacksonhodonnell@gmail.com
+    '''
+    if 'RBModels' not in data:
+        data['RBModels'] = {}
+    if 'MCSA' not in data:
+        data['MCSA'] = {'Models':[{'Type':'MD','Coef':[1.0,False,[.8,1.2],],'axis':[0,0,1]}],'Results':[],'AtInfo':{}}
+    if 'dict' in str(type(data['MCSA']['Results'])):
+        data['MCSA']['Results'] = []
+    if 'Modulated' not in data['General']:
+        data['General']['Modulated'] = False
+    if 'modulated' in data['General']['Type']:
+        data['General']['Modulated'] = True
+        data['General']['Type'] = 'nuclear'
+
+
+def SetupGeneral(data, dirname):
+    """Helps initialize phase data.
+
+    From GSASIIphsGui.py, function of the same name. Minor changes for imports etc.
+    Author: Jackson O'Donnell jacksonhodonnell@gmail.com
+    """
+    mapDefault = {'MapType':'','RefList':'','Resolution':0.5,'Show bonds':True,
+                'rho':[],'rhoMax':0.,'mapSize':10.0,'cutOff':50.,'Flip':False}
+    generalData = data['General']
+    atomData = data['Atoms']
+    generalData['AtomTypes'] = []
+    generalData['Isotopes'] = {}
+
+    if 'Isotope' not in generalData:
+        generalData['Isotope'] = {}
+    if 'Data plot type' not in generalData:
+        generalData['Data plot type'] = 'Mustrain'
+    if 'POhkl' not in generalData:
+        generalData['POhkl'] = [0,0,1]
+    if 'Map' not in generalData:
+        generalData['Map'] = mapDefault.copy()
+    if 'Flip' not in generalData:
+        generalData['Flip'] = {'RefList':'','Resolution':0.5,'Norm element':'None',
+            'k-factor':0.1,'k-Max':20.,}
+    if 'testHKL' not in generalData['Flip']:
+        generalData['Flip']['testHKL'] = [[0,0,2],[2,0,0],[1,1,1],[0,2,0],[1,2,3]]
+    if 'doPawley' not in generalData:
+        generalData['doPawley'] = False     #ToDo: change to ''
+    if 'Pawley dmin' not in generalData:
+        generalData['Pawley dmin'] = 1.0
+    if 'Pawley neg wt' not in generalData:
+        generalData['Pawley neg wt'] = 0.0
+    if 'Algolrithm' in generalData.get('MCSA controls',{}) or \
+        'MCSA controls' not in generalData:
+        generalData['MCSA controls'] = {'Data source':'','Annealing':[50.,0.001,50],
+        'dmin':2.0,'Algorithm':'log','Jump coeff':[0.95,0.5],'boltzmann':1.0,
+        'fast parms':[1.0,1.0,1.0],'log slope':0.9,'Cycles':1,'Results':[],'newDmin':True}
+    if 'AtomPtrs' not in generalData:
+        generalData['AtomPtrs'] = [3,1,7,9]
+        if generalData['Type'] == 'macromolecular':
+            generalData['AtomPtrs'] = [6,4,10,12]
+        elif generalData['Type'] == 'magnetic':
+            generalData['AtomPtrs'] = [3,1,10,12]
+    if generalData['Type'] in ['modulated',]:
+        generalData['Modulated'] = True
+        generalData['Type'] = 'nuclear'
+        if 'Super' not in generalData:
+            generalData['Super'] = 1
+            generalData['SuperVec'] = [[0,0,.1],False,4]
+            generalData['SSGData'] = {}
+        if '4DmapData' not in generalData:
+            generalData['4DmapData'] = mapDefault.copy()
+            generalData['4DmapData'].update({'MapType':'Fobs'})
+    if 'Modulated' not in generalData:
+        generalData['Modulated'] = False
+    if 'HydIds' not in generalData:
+        generalData['HydIds'] = {}
+    cx,ct,cs,cia = generalData['AtomPtrs']
+    generalData['NoAtoms'] = {}
+    generalData['BondRadii'] = []
+    generalData['AngleRadii'] = []
+    generalData['vdWRadii'] = []
+    generalData['AtomMass'] = []
+    generalData['Color'] = []
+    if generalData['Type'] == 'magnetic':
+        generalData['MagDmin'] = generalData.get('MagDmin',1.0)
+        landeg = generalData.get('Lande g',[])
+    generalData['Mydir'] = dirname
+    badList = {}
+    for iat,atom in enumerate(atomData):
+        atom[ct] = atom[ct].lower().capitalize()              #force to standard form
+        if generalData['AtomTypes'].count(atom[ct]):
+            generalData['NoAtoms'][atom[ct]] += atom[cx+3]*float(atom[cs+1])
+        elif atom[ct] != 'UNK':
+            Info = G2elem.GetAtomInfo(atom[ct])
+            if not Info:
+                if atom[ct] not in badList:
+                    badList[atom[ct]] = 0
+                badList[atom[ct]] += 1
+                atom[ct] = 'UNK'
+                continue
+            atom[ct] = Info['Symbol'] # N.B. symbol might be changed by GetAtomInfo
+            generalData['AtomTypes'].append(atom[ct])
+            generalData['Z'] = Info['Z']
+            generalData['Isotopes'][atom[ct]] = Info['Isotopes']
+            generalData['BondRadii'].append(Info['Drad'])
+            generalData['AngleRadii'].append(Info['Arad'])
+            generalData['vdWRadii'].append(Info['Vdrad'])
+            if atom[ct] in generalData['Isotope']:
+                if generalData['Isotope'][atom[ct]] not in generalData['Isotopes'][atom[ct]]:
+                    isotope = generalData['Isotopes'][atom[ct]].keys()[-1]
+                    generalData['Isotope'][atom[ct]] = isotope
+                generalData['AtomMass'].append(Info['Isotopes'][generalData['Isotope'][atom[ct]]]['Mass'])
+            else:
+                generalData['Isotope'][atom[ct]] = 'Nat. Abund.'
+                if 'Nat. Abund.' not in generalData['Isotopes'][atom[ct]]:
+                    isotope = generalData['Isotopes'][atom[ct]].keys()[-1]
+                    generalData['Isotope'][atom[ct]] = isotope
+                generalData['AtomMass'].append(Info['Mass'])
+            generalData['NoAtoms'][atom[ct]] = atom[cx+3]*float(atom[cs+1])
+            generalData['Color'].append(Info['Color'])
+            if generalData['Type'] == 'magnetic':
+                if len(landeg) < len(generalData['AtomTypes']):
+                    landeg.append(2.0)
+    if generalData['Type'] == 'magnetic':
+        generalData['Lande g'] = landeg[:len(generalData['AtomTypes'])]
+
+    if badList:
+        msg = 'Warning: element symbol(s) not found:'
+        for key in badList:
+            msg += '\n\t' + key
+            if badList[key] > 1:
+                msg += ' (' + str(badList[key]) + ' times)'
+        raise Exception("Phase error:\n" + msg)
+        # wx.MessageBox(msg,caption='Element symbol error')
+    F000X = 0.
+    F000N = 0.
+    for i,elem in enumerate(generalData['AtomTypes']):
+        F000X += generalData['NoAtoms'][elem]*generalData['Z']
+        isotope = generalData['Isotope'][elem]
+        F000N += generalData['NoAtoms'][elem]*generalData['Isotopes'][elem][isotope]['SL'][0]
+    generalData['F000X'] = F000X
+    generalData['F000N'] = F000N
+    generalData['Mass'] = G2mth.getMass(generalData)
+
+def make_empty_project(author=None, filename=None):
+    """Creates an dictionary in the style of GSASIIscriptable, for an empty
+    project.
+
+    If no author name or filename is supplied, 'no name' and
+    <current dir>/test_output.gpx are used , respectively.
+
+    Returns: project dictionary, name list
+    Author: Jackson O'Donnell jacksonhodonnell@gmail.com
+    """
+    if not filename:
+        filename = os.path.join(os.getcwd(), 'test_output.gpx')
+    else:
+        filename = os.path.abspath(filename)
+    gsasii_version = str(GSASIIpath.GetVersionNumber())
+    python_library_versions = G2fil.get_python_versions([mpl, np, sp])
+
+    controls_data = dict(G2obj.DefaultControls)
+    controls_data['LastSavedAs'] = unicode(filename)
+    controls_data['LastSavedUsing'] = gsasii_version
+    controls_data['PythonVersions'] = python_library_versions
+    if author:
+        controls_data['Author'] = author
+
+    output = {'Constraints': {'data': {'HAP': [], 'Hist': [], 'Phase': [],
+                                       'Global': []}},
+              'Controls': {'data': controls_data},
+              u'Covariance': {'data': {}},
+              u'Notebook': {'data': ['']},
+              u'Restraints': {'data': {}},
+              u'Rigid bodies': {'data': {'RBIds': {'Residue': [], 'Vector': []},
+                                'Residue': {'AtInfo': {}},
+                                'Vector':  {'AtInfo': {}}}}}
+
+    names = [[u'Notebook'], [u'Controls'], [u'Covariance'],
+             [u'Constraints'], [u'Restraints'], [u'Rigid bodies']]
+
+    return output, names
+
+
+class G2ImportException(Exception):
+    pass
+
+
+def import_generic(filename, readerlist):
+    """Attempt to import a filename, using a list of reader objects.
+
+    Returns the first reader object which worked."""
+    # Translated from OnImportGeneric method in GSASII.py
+    primaryReaders, secondaryReaders = [], []
+    for reader in readerlist:
+        flag = reader.ExtensionValidator(filename)
+        if flag is None:
+            secondaryReaders.append(reader)
+        elif flag:
+            primaryReaders.append(reader)
+    if not secondaryReaders and not primaryReaders:
+        raise G2ImportException("Could not read file: ", filename)
+
+    with open(filename, 'Ur') as fp:
+        rd_list = []
+
+        for rd in primaryReaders + secondaryReaders:
+            # Initialize reader
+            rd.selections = []
+            rd.dnames = []
+            rd.ReInitialize()
+            # Rewind file
+            fp.seek(0)
+            rd.errors = ""
+            if not rd.ContentsValidator(fp):
+                # Report error
+                pass
+            if len(rd.selections) > 1:
+                # Select data?
+                # GSASII.py:543
+                raise G2ImportException("Not sure what data to select")
+
+            block = 0
+            rdbuffer = {}
+            fp.seek(0)
+            repeat = True
+            while repeat:
+                repeat = False
+                block += 1
+                rd.objname = os.path.basename(filename)
+                flag = rd.Reader(filename, fp, buffer=rdbuffer, blocknum=block)
+                if flag:
+                    # Omitting image loading special cases
+                    rd.readfilename = filename
+                    rd_list.append(copy.deepcopy(rd))
+                    repeat = rd.repeat
+                else:
+                    raise G2ImportException("{}.Reader() returned:".format(rd),
+                                            flag)
+
+            if rd_list:
+                if rd.warnings:
+                    print("Read warning by", rd.formatName, "reader:",
+                          rd.warnings, file=sys.stderr)
+                return rd_list
+    raise G2ImportException("No reader could read file: " + filename)
+
+
+def load_iprms(instfile, reader):
+    """Loads instrument parameters from a file, and edits the
+    given reader.
+
+    Returns a 2-tuple of (Iparm1, Iparm2) parameters
+    """
+    ext = os.path.splitext(instfile)[1]
+
+    if ext.lower() == '.instprm':
+        # New GSAS File, load appropriately
+        with open(instfile) as f:
+            lines = f.readlines()
+        bank = reader.powderentry[2]
+        numbanks = reader.numbanks
+        iparms = G2fil.ReadPowderInstprm(lines, bank, numbanks, reader)
+
+        reader.instfile = instfile
+        reader.instmsg = 'GSAS-II file' + instfile
+        return iparms
+    elif ext.lower() not in ('.prm', '.inst', '.ins'):
+        raise ValueError('Expected .prm file, found: ', instfile)
+
+    # It's an old GSAS file, load appropriately
+    Iparm = {}
+    with open(instfile, 'Ur') as fp:
+        for line in fp:
+            if '#' in line:
+                continue
+            Iparm[line[:12]] = line[12:-1]
+    ibanks = int(Iparm.get('INS   BANK  ', '1').strip())
+    if ibanks == 1:
+        reader.instbank = 1
+        reader.powderentry[2] = 1
+        reader.instfile = instfile
+        reader.instmsg = instfile + ' bank ' + str(reader.instbank)
+        return G2fil.SetPowderInstParms(Iparm, reader)
+    # TODO handle >1 banks
+    raise NotImplementedError("Check GSASIIfiles.py: ReadPowderInstprm")
+
+def load_pwd_from_reader(reader, instprm, existingnames=[]):
+    """Loads powder data from a reader object, and assembles it into a GSASII data tree.
+
+    Returns: (name, tree) - 2-tuple of the histogram name (str), and data
+    Author: Jackson O'Donnell jacksonhodonnell@gmail.com
+    """
+    HistName = 'PWDR ' + G2obj.StripUnicode(reader.idstring, '_')
+    HistName = unicode(G2obj.MakeUniqueLabel(HistName, existingnames))
+
+    try:
+        Iparm1, Iparm2 = instprm
+    except ValueError:
+        Iparm1, Iparm2 = load_iprms(instprm, reader)
+
+    Ymin = np.min(reader.powderdata[1])
+    Ymax = np.max(reader.powderdata[1])
+    valuesdict = {'wtFactor': 1.0,
+                  'Dummy': False,
+                  'ranId': ran.randint(0, sys.maxint),
+                  'Offset': [0.0, 0.0], 'delOffset': 0.02*Ymax,
+                  'refOffset': -0.1*Ymax, 'refDelt': 0.1*Ymax,
+                  'qPlot': False, 'dPlot': False, 'sqrtPlot': False,
+                  'Yminmax': [Ymin, Ymax]}
+    reader.Sample['ranId'] = valuesdict['ranId']
+
+    # Ending keys:
+    # [u'Reflection Lists',
+    #  u'Limits',
+    #  'data',
+    #  u'Index Peak List',
+    #  u'Comments',
+    #  u'Unit Cells List',
+    #  u'Sample Parameters',
+    #  u'Peak List',
+    #  u'Background',
+    #  u'Instrument Parameters']
+    Tmin = np.min(reader.powderdata[0])
+    Tmax = np.max(reader.powderdata[0])
+
+    default_background = [['chebyschev', False, 3, 1.0, 0.0, 0.0],
+                          {'nDebye': 0, 'debyeTerms': [], 'nPeaks': 0, 'peaksList': []}]
+
+    output_dict = {u'Reflection Lists': {},
+                   u'Limits': reader.pwdparms.get('Limits', [(Tmin, Tmax), [Tmin, Tmax]]),
+                   u'data': [valuesdict, reader.powderdata, HistName],
+                   u'Index Peak List': [[], []],
+                   u'Comments': reader.comments,
+                   u'Unit Cells List': [],
+                   u'Sample Parameters': reader.Sample,
+                   u'Peak List': {'peaks': [], 'sigDict': {}},
+                   u'Background': reader.pwdparms.get('Background', default_background),
+                   u'Instrument Parameters': [Iparm1, Iparm2],
+                   }
+
+    names = [u'Comments',
+             u'Limits',
+             u'Background',
+             u'Instrument Parameters',
+             u'Sample Parameters',
+             u'Peak List',
+             u'Index Peak List',
+             u'Unit Cells List',
+             u'Reflection Lists']
+
+    # TODO controls?? GSASII.py:1664-7
+
+    return HistName, [HistName] + names, output_dict
+
+
+def _deep_copy_into(from_, into):
+    """Helper function for reloading .gpx file. See G2Project.reload()
+    Author: Jackson O'Donnell jacksonhodonnell@gmail.com
+    """
+    if isinstance(from_, dict) and isinstance(into, dict):
+        combined_keys = set(from_.keys()).union(into.keys())
+        for key in combined_keys:
+            if key in from_ and key in into:
+                both_dicts = (isinstance(from_[key], dict)
+                              and isinstance(into[key], dict))
+                both_lists = (isinstance(from_[key], list)
+                              and isinstance(into[key], list))
+                if both_dicts or both_lists:
+                    _deep_copy_into(from_[key], into[key])
+                else:
+                    into[key] = from_[key]
+            elif key in from_:
+                into[key] = from_[key]
+            else:  # key in into
+                del into[key]
+    elif isinstance(from_, list) and isinstance(into, list):
+        if len(from_) == len(into):
+            for i in xrange(len(from_)):
+                both_dicts = (isinstance(from_[i], dict)
+                              and isinstance(into[i], dict))
+                both_lists = (isinstance(from_[i], list)
+                              and isinstance(into[i], list))
+                if both_dicts or both_lists:
+                    _deep_copy_into(from_[i], into[i])
+                else:
+                    into[i] = from_[i]
+        else:
+            into[:] = from_
+
+
+class G2ObjectWrapper(object):
+    """Base class for all GSAS-II object wrappers.
+
+    The underlying GSAS-II format can be accessed as `wrapper.data`. A number
+    of overrides are implemented so that the wrapper behaves like a dictionary.
+
+    Author: Jackson O'Donnell jacksonhodonnell@gmail.com
+    """
+    def __init__(self, datadict):
+        self.data = datadict
+
+    def __getitem__(self, key):
+        return self.data[key]
+
+    def __setitem__(self, key, value):
+        self.data[key] = value
+
+    def __contains__(self, key):
+        return key in self.data
+
+    def get(self, k, d=None):
+        return self.data.get(k, d)
+
+    def keys(self):
+        return self.data.keys()
+
+    def values(self):
+        return self.data.values()
+
+    def items(self):
+        return self.data.items()
+
+
+class G2Project(G2ObjectWrapper):
+    def __init__(self, gpxfile=None, author=None, filename=None):
+        """Loads a GSAS-II project from a specified filename.
+
+        :param str gpxfile: Existing .gpx file to be loaded. If nonexistent,
+        creates an empty project.
+        :param str author: Author's name. Optional.
+        :param str filename: The filename the project should be saved to in
+        the future. If both filename and gpxfile are present, the project is
+        loaded from the gpxfile, then set to  save to filename in the future"""
+        if gpxfile is None:
+            filename = os.path.abspath(os.path.expanduser(filename))
+            self.filename = filename
+            self.data, self.names = make_empty_project(author=author, filename=filename)
+        elif isinstance(gpxfile, str):
+            # TODO set author, filename
+            self.filename = os.path.abspath(os.path.expanduser(gpxfile))
+            self.data, self.names = LoadDictFromProjFile(gpxfile)
+            self.index_ids()
+        else:
+            raise ValueError("Not sure what to do with gpxfile")
+
+    @classmethod
+    def from_dict_and_names(cls, gpxdict, names, filename=None):
+        """Creates a :class:`G2Project` directly from
+        a dictionary and a list of names. If in doubt, do not use this.
+
+        :returns: a :class:`G2Project`
+        """
+        out = cls()
+        if filename:
+            filename = os.path.abspath(os.path.expanduser(filename))
+            out.filename = filename
+            gpxdict['Controls']['data']['LastSavedAs'] = filename
+        else:
+            try:
+                out.filename = gpxdict['Controls']['data']['LastSavedAs']
+            except KeyError:
+                out.filename = None
+        out.data = gpxdict
+        out.names = names
+
+    def save(self, filename=None):
+        """Saves the project, either to the current filename, or to a new file.
+
+        Updates self.filename if a new filename provided"""
+        # TODO update LastSavedUsing ?
+        if filename:
+            filename = os.path.abspath(os.path.expanduser(filename))
+            self.data['Controls']['data']['LastSavedAs'] = filename
+            self.filename = filename
+        elif not self.filename:
+            raise AttributeError("No file name to save to")
+        SaveDictToProjFile(self.data, self.names, self.filename)
+
+    def add_powder_histogram(self, datafile, iparams):
+        """Loads a powder data histogram into the project.
+
+        Automatically checks for an instrument parameter file, or one can be
+        provided.
+
+        :param str datafile: The powder data file to read, a filename.
+        :param str iparams: The instrument parameters file, a filename.
+
+        :returns: A :class:`G2PwdrData` object representing
+        the histogram"""
+        datafile = os.path.abspath(os.path.expanduser(datafile))
+        iparams = os.path.abspath(os.path.expanduser(iparams))
+        pwdrreaders = import_generic(datafile, PwdrDataReaders)
+        histname, new_names, pwdrdata = load_pwd_from_reader(
+                                          pwdrreaders[0], iparams,
+                                          list(self.histogram_names()))
+        if histname in self.data:
+            print("Warning - redefining histogram", histname)
+        else:
+            if self.names[-1][0] == 'Phases':
+                self.names.insert(-1, new_names)
+            else:
+                self.names.append(new_names)
+        self.data[histname] = pwdrdata
+        return self.histogram(histname)
+
+    def add_phase(self, phasefile, phasename=None, histograms=[]):
+        """Loads a phase into the project from a .cif file
+
+        :param str phasefile: The CIF file from which to import the phase.
+        :param str phasename: The name of the new phase, or None for the default
+        :param list histograms: The names of the histograms to associate with
+        this phase
+
+        :returns: A :class:`G2Phase` object representing the
+        new phase."""
+        phasefile = os.path.abspath(os.path.expanduser(phasefile))
+
+        # TODO handle multiple phases in a file
+        phasereaders = import_generic(phasefile, PhaseReaders)
+        phasereader = phasereaders[0]
+
+        phasename = phasename or phasereader.Phase['General']['Name']
+        phaseNameList = list(self.phase_names())
+        phasename = G2obj.MakeUniqueLabel(phasename, phaseNameList)
+        phasereader.Phase['General']['Name'] = phasename
+
+        if 'Phases' not in self.data:
+            self.data[u'Phases'] = { 'data': None }
+        assert phasename not in self.data['Phases'], "phase names should be unique"
+        self.data['Phases'][phasename] = phasereader.Phase
+
+        if phasereader.Constraints:
+            Constraints = self.data['Constraints']
+            for i in phasereader.Constraints:
+                if isinstance(i, dict):
+                    if '_Explain' not in Constraints:
+                        Constraints['_Explain'] = {}
+                    Constraints['_Explain'].update(i)
+                else:
+                    Constraints['Phase'].append(i)
+
+        data = self.data['Phases'][phasename]
+        generalData = data['General']
+        SGData = generalData['SGData']
+        NShkl = len(G2spc.MustrainNames(SGData))
+        NDij = len(G2spc.HStrainNames(SGData))
+        Super = generalData.get('Super', 0)
+        if Super:
+            SuperVec = np.array(generalData['SuperVec'][0])
+        else:
+            SuperVec = []
+        UseList = data['Histograms']
+
+        for histname in histograms:
+            if histname.startswith('HKLF '):
+                raise NotImplementedError("Does not support HKLF yet")
+            elif histname.startswith('PWDR '):
+                hist = self.histogram(histname)
+                hist['Reflection Lists'][generalData['Name']] = {}
+                UseList[histname] = SetDefaultDData('PWDR', histname, NShkl=NShkl, NDij=NDij)
+                for key, val in [('Use', True), ('LeBail', False),
+                                 ('newLeBail', True),
+                                 ('Babinet', {'BabA': [0.0, False],
+                                              'BabU': [0.0, False]})]:
+                    if key not in UseList[histname]:
+                        UseList[histname][key] = val
+            else:
+                raise NotImplementedError("Unexpected histogram" + histname)
+
+        for obj in self.names:
+            if obj[0] == 'Phases':
+                phasenames = obj
+                break
+        else:
+            phasenames = [u'Phases']
+            self.names.append(phasenames)
+        phasenames.append(unicode(phasename))
+
+        # TODO should it be self.filename, not phasefile?
+        SetupGeneral(data, os.path.dirname(phasefile))
+        self.index_ids()
+
+        return self.phase(phasename)
+
+    def reload(self):
+        """Reload self from self.filename"""
+        data, names = LoadDictFromProjFile(self.filename)
+        self.names = names
+        # Need to deep copy the new data file data into the current tree,
+        # so that any existing G2Phase, or G2PwdrData objects will still be
+        # valid
+        _deep_copy_into(from_=data, into=self.data)
+
+    def refine(self, newfile=None, printFile=None):
+        # index_ids will automatically save the project
+        self.index_ids()
+        # TODO G2strMain does not properly use printFile
+        G2strMain.Refine(self.filename)
+        # Reload yourself
+        self.reload()
+
+    def histogram_names(self):
+        """Gives a list of the names of each histogram in the project.
+
+        :returns: list of strings
+
+        .. seealso::
+            :func:`~GSASIIscriptable.G2Project.histogram`
+            :func:`~GSASIIscriptable.G2Project.histograms`
+            :func:`~GSASIIscriptable.G2Project.phase`
+            :func:`~GSASIIscriptable.G2Project.phases`
+            :func:`~GSASIIscriptable.G2Project.phase_names`
+            """
+        output = []
+        for obj in self.names:
+            if len(obj) > 1 and obj[0] != u'Phases':
+                output.append(obj[0])
+        return output
+
+    def histogram(self, histname):
+        """Returns the histogram named histname, or None if it does not exist.
+
+        :returns: A :class:`G2PwdrData` object, or None if
+        the histogram does not exist
+        .. seealso::
+            :func:`~GSASIIscriptable.G2Project.histogram_names`
+            :func:`~GSASIIscriptable.G2Project.histograms`
+            :func:`~GSASIIscriptable.G2Project.phase`
+            :func:`~GSASIIscriptable.G2Project.phases`
+            :func:`~GSASIIscriptable.G2Project.phase_names`
+            """
+        if histname in self.data:
+            return G2PwdrData(self.data[histname], self)
+        return None
+
+    def histograms(self):
+        """Return a list of all histograms, as
+        :class:`G2PwdrData` objects
+        .. seealso::
+            :func:`~GSASIIscriptable.G2Project.histogram_names`
+            :func:`~GSASIIscriptable.G2Project.histograms`
+            :func:`~GSASIIscriptable.G2Project.phase`
+            :func:`~GSASIIscriptable.G2Project.phases`
+            :func:`~GSASIIscriptable.G2Project.phase_names`
+            """
+        return [self.histogram(name) for name in self.histogram_names()]
+
+    def phase_names(self):
+        """Gives an list of the names of each phase in the project.
+
+        :returns: A list of strings
+        .. seealso::
+            :func:`~GSASIIscriptable.G2Project.histogram`
+            :func:`~GSASIIscriptable.G2Project.histograms`
+            :func:`~GSASIIscriptable.G2Project.histogram_names`
+            :func:`~GSASIIscriptable.G2Project.phase`
+            :func:`~GSASIIscriptable.G2Project.phases`
+            """
+        for obj in self.names:
+            if obj[0] == 'Phases':
+                return obj[1:]
+        return []
+
+    def phase(self, phasename):
+        """
+        Gives an object representing the specified phase in this project.
+
+        :param str phasename: The name of the desired phase
+        :returns: A :class:`G2Phase` object
+        :raises: KeyError
+        .. seealso::
+            :func:`~GSASIIscriptable.G2Project.histogram_names`
+            :func:`~GSASIIscriptable.G2Project.histograms`
+            :func:`~GSASIIscriptable.G2Project.phase`
+            :func:`~GSASIIscriptable.G2Project.phases`
+            :func:`~GSASIIscriptable.G2Project.phase_names`
+            """
+        phases = self.data['Phases']
+        if phasename in phases:
+            return G2Phase(phases[phasename], phasename, self)
+
+    def phases(self):
+        """
+        Returns a list of all the phases in the project.
+
+        :returns: A :class:`G2Phase`
+        .. seealso::
+            :func:`~GSASIIscriptable.G2Project.histogram`
+            :func:`~GSASIIscriptable.G2Project.histograms`
+            :func:`~GSASIIscriptable.G2Project.histogram_names`
+            :func:`~GSASIIscriptable.G2Project.phase`
+            :func:`~GSASIIscriptable.G2Project.phase_names`
+            """
+        return [self.phase(name) for name in self.phase_names()]
+
+    def do_refinements(self, refinements, histogram='all', phase='all',
+                       outputnames=None):
+        """Conducts a series of refinements.
+
+        :param list refinements: A list of dictionaries defining refinements
+        :param str histogram: Name of histogram for refinements to be applied
+        to, or 'all'
+        :param str phase: Name of phase for refinements to be applied to, or
+        'all'
+        """
+        if outputnames:
+            if len(refinements) != len(outputnames):
+                raise ValueError("Should have same number of outuputs to"
+                                 "refinements")
+        else:
+            outputnames = [None for r in refinements]
+
+        for output, refinement in zip(outputnames, refinements):
+            self.set_refinement(refinement, histogram)
+            # Handle 'once' args - refinements that are disabled after this
+            # refinement
+            if 'once' in refinement:
+                temp = {'set': refinement['once']}
+                self.set_refinement(temp, histogram, phase)
+
+            if output:
+                self.save(output)
+
+            self.refine()  # newFile=output)
+
+            # Handle 'once' args - refinements that are disabled after this
+            # refinement
+            if 'once' in refinement:
+                temp = {'clear': refinement['once']}
+                self.set_refinement(temp, histogram, phase)
+
+    def set_refinement(self, refinement, histogram='all', phase='all'):
+        """Apply specified refinements to a given histogram(s) or phase(s).
+
+        :param dict refinement: The refinements to be conducted
+        :param histogram: Either a name of a histogram (str), a list of
+        histogram names, or 'all' (default)
+        :param phase: Either a name of a phase (str), a list of phase names, or
+        'all' (default)"""
+        if histogram == 'all':
+            hists = [self.histogram(name)
+                     for name in self.histogram_names()]
+        elif isinstance(histogram, str):
+            hists = [self.histogram(histogram)]
+        else:
+            hists = [self.histogram(name) for name in histogram]
+
+        if phase == 'all':
+            phases = [self.phase(name) for name in self.phase_names()]
+        elif isinstance(phase, str):
+            phases = [self.phase(phase)]
+        else:
+            phases = [self.phase(name) for name in phase]
+
+
+        # TODO: HAP parameters:
+        #   Babinet
+        #   Extinction
+        #   HStrain
+        #   Mustrain
+        #   Pref. Ori
+        #   Size
+
+        pwdr_set = {}
+        phase_set = {}
+        for key, val in refinement.get('set', {}).items():
+            # Apply refinement options
+            if G2PwdrData.is_valid_refinement_key(key):
+                pwdr_set[key] = val
+            elif G2Phase.is_valid_refinement_key(key):
+                phase_set[key] = val
+            else:
+                print("Unknown refinement key:", key)
+
+        for hist in hists:
+            hist.set_refinements(pwdr_set)
+        for phase in phases:
+            phase.set_refinements(phase_set)
+
+        pwdr_clear = {}
+        phase_clear = {}
+        for key, val in refinement.get('clear', {}).items():
+            # Clear refinement options
+            if G2PwdrData.is_valid_refinement_key(key):
+                pwdr_clear[key] = val
+            elif G2Phase.is_valid_refinement_key(key):
+                phase_clear[key] = val
+            else:
+                print("Unknown refinement key:", key)
+
+        for hist in hists:
+            hist.clear_refinements(pwdr_clear)
+        for phase in phases:
+            phase.clear_refinements(phase_clear)
+
+    def index_ids(self):
+        self.save()
+        return G2strIO.GetUsedHistogramsAndPhases(self.filename)
+
+    def add_constraint_raw(self, cons_scope, constr):
+        """Adds a constraint of type consType to the project.
+        cons_scope should be one of "Hist", "Phase", "HAP", or "Global".
+
+        WARNING it does not check the constraint is well-constructed"""
+        constrs = self['Constraints']['data']
+        if 'Global' not in constrs:
+            constrs['Global'] = []
+        constrs[cons_scope].append(constr)
+
+    def hold_many(self, vars, type):
+        """Apply holds for all the variables in vars, for constraint of a given type.
+
+        type is passed directly to add_constraint_raw as consType
+
+        :param list vars: A list of variables to hold. Either G2obj.G2VarObj objects,
+        string variable specifiers, or arguments for :meth:`make_var_obj`
+        :param str type: A string constraint type specifier. See
+        :class:`~GSASIIscriptable.G2Project.add_constraint_raw`"""
+        for var in vars:
+            if isinstance(var, str):
+                var = self.make_var_obj(var)
+            elif not isinstance(var, G2obj.G2VarObj):
+                var = self.make_var_obj(*var)
+            self.add_constraint_raw(type, [[1.0, var], None, None, 'h'])
+
+    def make_var_obj(self, phase=None, hist=None, varname=None, atomId=None,
+                     reloadIdx=True):
+        """Wrapper to create a G2VarObj. Takes either a string representaiton ("p:h:name:a")
+        or individual names of phase, histogram, varname, and atomId.
+
+        Automatically converts string phase, hist, or atom names into the ID required
+        by G2VarObj."""
+        if reloadIdx:
+            self.index_ids()
+
+        # If string representation, short circuit
+        if hist is None and varname is None and atomId is None:
+            if isinstance(phase, str) and ':' in phase:
+                return G2obj.G2VarObj(phase)
+
+        # Get phase index
+        phaseObj = None
+        if isinstance(phase, G2Phase):
+            phaseObj = phase
+            phase = G2obj.PhaseRanIdLookup[phase.ranId]
+        elif phase in self['Phases']:
+            phaseObj = self.phase(phase)
+            phaseRanId = phaseObj.ranId
+            phase = G2obj.PhaseRanIdLookup[phaseRanId]
+
+        # Get histogram index
+        if isinstance(hist, G2PwdrData):
+            hist = G2obj.HistRanIdLookup[hist.ranId]
+        elif hist in self.data:
+            histRanId = self.histogram(hist).ranId
+            hist = G2obj.HistRanIdLookup[histRanId]
+
+        # Get atom index (if any)
+        if isinstance(atomId, G2AtomRecord):
+            atomId = G2obj.AtomRanIdLookup[phase][atomId.ranId]
+        elif phaseObj:
+            atomObj = phaseObj.atom(atomId)
+            if atomObj:
+                atomRanId = atomObj.ranId
+                atomId = G2obj.AtomRanIdLookup[phase][atomRanId]
+
+        return G2obj.G2VarObj(phase, hist, varname, atomId)
+
+
+class G2AtomRecord(G2ObjectWrapper):
+    """Wrapper for an atom record. Has convenient accessors via @property.
+
+    Example:
+
+    >>> atom = some_phase.atom("O3")
+    >>> # We can access the underlying data format
+    >>> atom.data
+    ['O3', 'O-2', '', ... ]
+    >>> # We can also use wrapper accessors
+    >>> atom.coordinates
+    (0.33, 0.15, 0.5)
+    >>> atom.refinement_flags
+    u'FX'
+    >>> atom.ranId
+    4615973324315876477
+    """
+    def __init__(self, data, indices, proj):
+        self.data = data
+        self.cx, self.ct, self.cs, self.cia = indices
+        self.proj = proj
+
+    @property
+    def label(self):
+        return self.data[self.ct-1]
+
+    @property
+    def type(self):
+        return self.data[self.ct]
+
+    @property
+    def refinement_flags(self):
+        return self.data[self.ct+1]
+
+    @refinement_flags.setter
+    def refinement_flags(self, other):
+        # Automatically check it is a valid refinement
+        for c in other:
+            if c not in ' FXU':
+                raise ValueError("Invalid atom refinement: ", other)
+        self.data[self.ct+1] = unicode(other)
+
+    @property
+    def coordinates(self):
+        return tuple(self.data[self.cx:self.cx+3])
+
+    @property
+    def ranId(self):
+        return self.data[self.cia+8]
+
+    @property
+    def adp_flag(self):
+        # Either 'I' or 'A'
+        return self.data[self.cia]
+
+    @property
+    def uiso(self):
+        if self.adp_flag == 'I':
+            return self.data[self.cia+1]
+        else:
+            return self.data[self.cia+2:self.cia+8]
+
+
+class G2PwdrData(G2ObjectWrapper):
+    """Wraps a Poweder Data Histogram."""
+    def __init__(self, data, proj):
+        self.data = data
+        self.proj = proj
+
+    @staticmethod
+    def is_valid_refinement_key(key):
+        valid_keys = ['Limits', 'Sample Parameters', 'Background',
+                      'Instrument Parameters']
+        return key in valid_keys
+
+    @property
+    def name(self):
+        return self['data'][-1]
+
+    @property
+    def ranId(self):
+        return self['data'][0]['ranId']
+
+    @property
+    def residuals(self):
+        data = self['data'][0]
+        return {key: data[key]
+                for key in ['R', 'Rb', 'wR', 'wRb', 'wRmin']}
+
+    def fit_fixed_points(self):
+        """Attempts to apply a background fit to the fixed points currently specified."""
+
+        def SetInstParms(Inst):
+            dataType = Inst['Type'][0]
+            insVary = []
+            insNames = []
+            insVals = []
+            for parm in Inst:
+                insNames.append(parm)
+                insVals.append(Inst[parm][1])
+                if parm in ['U','V','W','X','Y','SH/L','I(L2)/I(L1)','alpha',
+                    'beta-0','beta-1','beta-q','sig-0','sig-1','sig-2','sig-q',] and Inst[parm][2]:
+                        Inst[parm][2] = False
+            instDict = dict(zip(insNames, insVals))
+            instDict['X'] = max(instDict['X'], 0.01)
+            instDict['Y'] = max(instDict['Y'], 0.01)
+            if 'SH/L' in instDict:
+                instDict['SH/L'] = max(instDict['SH/L'], 0.002)
+            return dataType, instDict, insVary
+
+        bgrnd = self['Background']
+
+        # Need our fixed points in order
+        bgrnd[1]['FixedPoints'].sort(key=lambda pair: pair[0])
+        X = [x for x, y in bgrnd[1]['FixedPoints']]
+        Y = [y for x, y in bgrnd[1]['FixedPoints']]
+
+        limits = self['Limits'][1]
+        if X[0] > limits[0]:
+            X = [limits[0]] + X
+            Y = [Y[0]] + Y
+        if X[-1] < limits[1]:
+            X += [limits[1]]
+            Y += [Y[-1]]
+
+        # Some simple lookups
+        controls = self.proj['Controls']['data']
+        inst, inst2 = self['Instrument Parameters']
+        pwddata = self['data'][1]
+
+        # Construct the data for background fitting
+        xBeg = np.searchsorted(pwddata[0], limits[0])
+        xFin = np.searchsorted(pwddata[0], limits[1])
+        xdata = pwddata[0][xBeg:xFin]
+        ydata = si.interp1d(X,Y)(ma.getdata(xdata))
+
+        W = [1]*len(xdata)
+        Z = [0]*len(xdata)
+
+        dataType, insDict, insVary = SetInstParms(inst)
+        bakType, bakDict, bakVary = G2pwd.SetBackgroundParms(bgrnd)
+
+        # Do the fit
+        data = np.array([xdata, ydata, W, Z, Z, Z])
+        G2pwd.DoPeakFit('LSQ', [], bgrnd, limits, inst, inst2, data,
+                        prevVaryList=bakVary, controls=controls)
+
+        # Post-fit
+        parmDict = {}
+        bakType, bakDict, bakVary = G2pwd.SetBackgroundParms(bgrnd)
+        parmDict.update(bakDict)
+        parmDict.update(insDict)
+        pwddata[3][xBeg:xFin] *= 0
+        pwddata[5][xBeg:xFin] *= 0
+        pwddata[4][xBeg:xFin] = G2pwd.getBackground('', parmDict, bakType, dataType, xdata)[0]
+
+        # TODO adjust pwddata? GSASIIpwdGUI.py:1041
+        # TODO update background
+        self.proj.save()
+
+    def y_calc(self):
+        return self['data'][1][3]
+
+    def plot(self, Yobs=True, Ycalc=True, Background=True, Residual=True):
+        if plt:
+            data = self['data'][1]
+            if Yobs:
+                plt.plot(data[0], data[1], label='Yobs')
+            if Ycalc:
+                plt.plot(data[0], data[3], label='Ycalc')
+            if Background:
+                plt.plot(data[0], data[4], label='Background')
+            if Residual:
+                plt.plot(data[0], data[5], label="Residual")
+
+    def set_refinements(self, refs):
+        """Sets the refinement parameter 'key' to the specification 'value'
+
+        :param dict refs: A dictionary of the parameters to be set.
+
+        :returns: None"""
+        do_fit_fixed_points = False
+        for key, value in refs.items():
+            if key == 'Limits':
+                old_limits = self.data['Limits'][1]
+                new_limits = value
+                if isinstance(new_limits, dict):
+                    if 'low' in new_limits:
+                        old_limits[0] = new_limits['low']
+                    if 'high' in new_limits:
+                        old_limits[1] = new_limits['high']
+                else:
+                    old_limits[0], old_limits[1] = new_limits
+            elif key == 'Sample Parameters':
+                sample = self.data['Sample Parameters']
+                for sparam in value:
+                    sample[sparam][1] = True
+            elif key == 'Background':
+                bkg, peaks = self.data['Background']
+
+                # If True or False, just set the refine parameter
+                if value in (True, False):
+                    bkg[1] = value
+                    return
+
+                if 'type' in value:
+                    bkg[0] = value['type']
+                if 'refine' in value:
+                    bkg[1] = value['refine']
+                if 'no. coeffs' in value:
+                    cur_coeffs = bkg[2]
+                    n_coeffs = value['no. coeffs']
+                    if n_coeffs > cur_coeffs:
+                        for x in range(n_coeffs - cur_coeffs):
+                            bkg.append(0.0)
+                    else:
+                        for _ in range(cur_coeffs - n_coeffs):
+                            bkg.pop()
+                    bkg[2] = n_coeffs
+                if 'coeffs' in value:
+                    bkg[3:] = value['coeffs']
+                if 'FixedPoints' in value:
+                    peaks['FixedPoints'] = [(float(a), float(b))
+                                            for a, b in value['FixedPoints']]
+                if value.get('fit fixed points', False):
+                    do_fit_fixed_points = True
+
+            elif key == 'Instrument Parameters':
+                instrument, secondary = self.data['Instrument Parameters']
+                for iparam in value:
+                    try:
+                        instrument[iparam][2] = True
+                    except IndexError:
+                        raise ValueError("Invalid key:", iparam)
+            else:
+                raise ValueError("Unknown key:", key)
+        # Fit fixed points after the fact - ensure they are after fixed points
+        # are added
+        if do_fit_fixed_points:
+            # Background won't be fit if refinement flag not set
+            orig = self['Background'][0][1]
+            self['Background'][0][1] = True
+            self.fit_fixed_points()
+            # Restore the previous value
+            self['Background'][0][1] = orig
+
+    def clear_refinements(self, refs):
+        """Clears the refinement parameter 'key' and its associated value."""
+        for key, value in refs.items():
+            if key == 'Limits':
+                old_limits, cur_limits = self.data['Limits']
+                cur_limits[0], cur_limits[1] = old_limits
+            elif key == 'Sample Parameters':
+                sample = self.data['Sample Parameters']
+                for sparam in value:
+                    sample[sparam][1] = False
+            elif key == 'Background':
+                bkg, peaks = self.data['Background']
+
+                # If True or False, just set the refine parameter
+                if value in (True, False):
+                    bkg[1] = False
+                    return
+
+                bkg[1] = False
+                if 'FixedPoints' in value:
+                    if 'FixedPoints' in peaks:
+                        del peaks['FixedPoints']
+            elif key == 'Instrument Parameters':
+                instrument, secondary = self.data['Instrument Parameters']
+                for iparam in value:
+                    instrument[iparam][2] = False
+            else:
+                raise ValueError("Unknown key:", key)
+
+
+class G2Phase(G2ObjectWrapper):
+    """A wrapper object around a given phase.
+    Author: Jackson O'Donnell jacksonhodonnell@gmail.com
+    """
+    def __init__(self, data, name, proj):
+        self.data = data
+        self.name = name
+        self.proj = proj
+
+    @staticmethod
+    def is_valid_refinement_key(key):
+        valid_keys = ["Cell", "Atoms", "LeBail"]
+        return key in valid_keys
+
+    @staticmethod
+    def is_valid_HAP_refinement_key(key):
+        valid_keys = ["Babinet", "Extinction", "HStrain", "Mustrain",
+                      "Pref.Ori.", "Show", "Size", "Use", "Scale"]
+        return key in valid_keys
+
+    def atom(self, atomlabel):
+        """Returns the atom specified by atomlabel, or None if it does not
+        exist.
+
+        :param str atomlabel: The name of the atom (e.g. "O2")
+
+        :returns: A :class:`G2AtomRecord` object
+        representing the atom."""
+        # Consult GSASIIobj.py for the meaning of this
+        cx, ct, cs, cia = self.data['General']['AtomPtrs']
+        ptrs = [cx, ct, cs, cia]
+        atoms = self.data['Atoms']
+        for atom in atoms:
+            if atom[ct-1] == atomlabel:
+                return G2AtomRecord(atom, ptrs, self.proj)
+
+    def atoms(self):
+        """Returns a list of atoms present in the phase.
+
+        :returns: A list of :class:`G2AtomRecord` objects. See
+        also :func:`~GSASIIscriptable.G2Phase.atom`"""
+        ptrs = self.data['General']['AtomPtrs']
+        output = []
+        atoms = self.data['Atoms']
+        for atom in atoms:
+            output.append(G2AtomRecord(atom, ptrs, self.proj))
+        return output
+
+    def histograms(self):
+        output = []
+        for hname in self.data.get('Histograms', {}).keys():
+            output.append(self.proj.histogram(hname))
+        return output
+
+    @property
+    def ranId(self):
+        return self.data['ranId']
+
+    def cell_dict(self):
+        """Returns a dictionary of the cell parameters, with keys:
+            'a', 'b', 'c', 'alpha', 'beta', 'gamma', 'vol'
+
+        :returns: a dict"""
+        cell = self['General']['Cell']
+        return {'a': cell[1], 'b': cell[2], 'c': cell[3],
+                'alpha': cell[4], 'beta': cell[5], 'gamma': cell[6],
+                'vol': cell[7]}
+
+    def set_refinements(self, refs):
+        for key, value in refs.items():
+            if key == "Cell":
+                self.data['General']['Cell'][0] = True
+            elif key == "Atoms":
+                cx, ct, cs, cia = self.data['General']['AtomPtrs']
+
+                for atomlabel, atomrefinement in value.items():
+                    if atomlabel == 'all':
+                        for atom in self.atoms():
+                            atom.refinement_flags = atomrefinement
+                    else:
+                        atom = self.atom(atomlabel)
+                        atom.refinement_flags = atomrefinement
+            elif key == "LeBail":
+                hists = self.data['Histograms']
+                for hname, hoptions in hists.items():
+                    if 'LeBail' not in hoptions:
+                        hoptions['newLeBail'] = True
+                    hoptions['LeBail'] = bool(value)
+            else:
+                raise ValueError("Unknown key:", key)
+
+    def clear_refinements(self, refs):
+        for key, value in refs.items():
+            if key == "Cell":
+                self.data['General']['Cell'][0] = False
+            elif key == "Atoms":
+                cx, ct, cs, cia = self.data['General']['AtomPtrs']
+
+                for atomlabel in value:
+                    atom = self.atom(atomlabel)
+                    # Set refinement to none
+                    atom.refinement_flags = ' '
+            elif key == "LeBail":
+                hists = self.data['Histograms']
+                for hname, hoptions in hists.items():
+                    if 'LeBail' not in hoptions:
+                        hoptions['newLeBail'] = True
+                    hoptions['LeBail'] = False
+            else:
+                raise ValueError("Unknown key:", key)
+
+
+##########################
+# Command Line Interface #
+##########################
+
+
+def create(*args):
+    """The create subcommand.
+
+    Should be passed all the command-line arguments after `create`"""
+    proj = G2Project(filename=args[0])
+
+    isPhase = False
+    isPowderData = False
+    isInstPrms = False
+    instPrms = None
+
+    # TODO how to associate phase with histogram?
+    for arg in args[1:]:
+        if arg == '--phases':
+            isPhase = True
+            isPowderData = False
+            isInstPrms = False
+        elif arg == '--powder':
+            isPhase = False
+            isPowderData = True
+            isInstPrms = False
+        # Instrument parameters must be specified before
+        # any powder data files are passed
+        elif arg == '--iparams':
+            isPhase = False
+            isPowderData = False
+            isInstPrms = True
+        elif isPhase:
+            proj.add_phase(arg)
+        elif isPowderData:
+            proj.add_powder_histogram(arg, instPrms)
+        elif isInstPrms:
+            instPrms = arg
+            isInstPrms = False
+        else:
+            print("Not sure what to do with: {}".format(arg))
+
+    proj.save()
+
+
+def dump(*args):
+    """The dump subcommand"""
+    raw = True
+    histograms = False
+    phases = False
+    filenames = []
+    for arg in args:
+        if arg in ['-h', '--histograms']:
+            histograms = True
+            raw = False
+        elif arg in ['-p', '--phases']:
+            phases = True
+            raw = False
+        elif arg in ['-r', '--raw']:
+            raw = True
+        else:
+            filenames.append(arg)
+    if raw:
+        import IPython.lib.pretty as pretty
+    for fname in filenames:
+        if raw:
+            proj, nameList = LoadDictFromProjFile(fname)
+            print("file:", fname)
+            print("names:", nameList)
+            for key, val in proj.items():
+                print(key, ":")
+                pretty.pprint(val)
+        else:
+            proj = G2Project(fname)
+            if histograms:
+                hists = proj.histograms()
+                for h in hists:
+                    print(fname, h.name)
+            if phases:
+                phases = proj.phases()
+                for p in phases:
+                    print(fname, p.name)
+
+
+def IPyBrowse(*args):
+    """Load a .gpx file and then open a IPython shell to browse it
+    """
+    filename = []
+    for arg in args:
+        fname = arg
+        proj, nameList = LoadDictFromProjFile(fname)
+        msg = "\nfile {} loaded into proj (dict) with names in nameList".format(fname)
+        GSASIIpath.IPyBreak_base(msg)
+        break
+
+
+def refine(*args):
+    """The refine subcommand"""
+    proj = G2Project(args[0])
+    proj.refine()
+
+
+def seqrefine(*args):
+    """The seqrefine subcommand"""
+    raise NotImplementedError("seqrefine is not yet implemented")
+
+
+def export(*args):
+    """The export subcommand"""
+    # Export CIF or Structure or ...
+    raise NotImplementedError("export is not yet implemented")
+
+
+subcommands = {"create": create,
+               "dump": dump,
+               "refine": refine,
+               "seqrefine": seqrefine,
+               "export": export,
+               "browse": IPyBrowse}
+
 
 def main():
-    'Needs a doc string'
-    arg = sys.argv
-    print arg
-    if len(arg) > 1:
-        GPXfile = arg[1]
-        if not ospath.exists(GPXfile):
-            print 'ERROR - ',GPXfile," doesn't exist!"
-            exit()
-        Project,nameList = LoadDictFromProjFile(GPXfile)
-        SaveDictToProjFile(Project,nameList,'testout.gpx')
+    '''TODO: the command-line options need some thought
+    '''
+    argv = sys.argv
+    if len(argv) > 1 and argv[1] in subcommands:
+        subcommands[argv[1]](*argv[2:])
+    elif len(argv) == 1 or argv[1] in ('help', '--help', '-h'):
+        # TODO print usage
+        subcommand_names = ' | '.join(sorted(subcommands.keys()))
+        print("USAGE: {} [ {} ] ...".format(argv[0], subcommand_names))
     else:
-        print 'ERROR - missing filename'
-        exit()
-    print "Done"
-         
+        print("Unknown subcommand: {}".format(argv[1]))
+        print("Available subcommands:")
+        for name in sorted(subcommands.keys()):
+            print("\t{}".format(name))
+        sys.exit(-1)
+    # arg = sys.argv
+    # print(arg)
+    # if len(arg) > 1:
+    #     GPXfile = arg[1]
+    #     if not ospath.exists(GPXfile):
+    #         print(u'ERROR - '+GPXfile+u" doesn't exist!")
+    #         exit()
+    #     Project,nameList = LoadDictFromProjFile(GPXfile)
+    #     SaveDictToProjFile(Project,nameList,'testout.gpx')
+    # else:
+    #     print('ERROR - missing filename')
+    #     exit()
+    # print("Done")
+
+PwdrDataReaders = G2fil.LoadImportRoutines("pwd", "Powder_Data")
+PhaseReaders = G2fil.LoadImportRoutines("phase", "Phase")
 if __name__ == '__main__':
     main()
+
+    # from gpx_manipulatons.py
+    # try:
+    #     filename, authorname = sys.argv[1:3]
+    #     proj, names = make_empty_project(authorname, filename)
+    #     SaveDictToProjFile(proj, names, os.path.abspath(filename))
+    # except ValueError:
+    #     print("Usage: {} <filename> <author>".format(sys.argv[0]))
+    #     sys.exit(-1)
+
+
+    # from refinements.py
+#      USAGE = """USAGE: {} datafile instparams phasefile projectname refinements
+
+# datafile:    Input powder data
+# intparams:   Corresponding instrument parameter file
+# phasefile:   Phase to refine against data
+# projectname: Project file to be created, should end in .gpx
+# refinements: JSON file of refinements to be executed
+# """
+#     try:
+#         datafile, instprm, phasefile, projectname, refinements = sys.argv[1:]
+#     except ValueError:
+#         print(USAGE.format(sys.argv[0]))
+#         sys.exit(-1)
+
+#     try:
+#         with open(refinements) as f:
+#             refinements = json.load(f)
+#     except IOError:
+#         print("No such refinements file: {}".format(refinements))
+
+#     print("Creating project file \"{}\"...".format(projectname))
+#     proj = G2Project(filename=projectname)
+#     # Add the histogram
+#     hist = proj.add_powder_histogram(datafile, instprm)
+#     # Add the phase, and associate it with the histogram
+#     proj.add_phase(phasefile, histograms=[hist.name])
+
+#     proj.do_refinements(refinements['refinements'])
+#     proj.save()
+
+
+    # from gpx_dumper
+    # import IPython.lib.pretty as pretty
+    # proj, nameList = LoadDictFromProjFile(sys.argv[1])
+    # print("names:", nameList)
+    # for key, val in proj.items():
+    #     print(key, ":", sep='')
+    #     pretty.pprint(val)
+