Changeset 981

Timestamp:

Jul 7, 2013 9:58:08 AM (10 years ago)

Author:

toby

Message:

introduce regress option; fix esd printing; more docs; new Mac app with drag & drop for open; control reset of ref list on load

Location:

trunk

Files:

• GSASIIIO.py (modified) (1 diff)
• GSASIIgrid.py (modified) (4 diffs)
• GSASIImath.py (modified) (2 diffs)
• GSASIIobj.py (modified) (3 diffs)
• GSASIIpath.py (modified) (6 diffs)
• GSASIIstrIO.py (modified) (2 diffs)
• exports/G2cif.py (modified) (7 diffs)
• gsas2.icns (added)
• makeMacApp.py (added)

trunk/GSASIIIO.py

@@ -1594 +1594 @@
             Phases,RestraintDict=None,rbIds=rbIds,Print=False)
         self.parmDict.update(phaseDict)
-        hapVary,hapDict,controlDict =  G2stIO.GetHistogramPhaseData(Phases,Histograms,Print=False)
+        hapVary,hapDict,controlDict =  G2stIO.GetHistogramPhaseData(
+            Phases,Histograms,Print=False,resetRefList=False)
         self.parmDict.update(hapDict)
         histVary,histDict,controlDict =  G2stIO.GetHistogramData(Histograms,Print=False)

trunk/GSASIIgrid.py

@@ -1151 +1151 @@
 
 ################################################################################
+class downdate(wx.Dialog):
+    '''Dialog to allow a user to select a version of GSAS-II to install
+    '''
+    def __init__(self,parent=None):
+        style=wx.DEFAULT_DIALOG_STYLE | wx.RESIZE_BORDER
+        wx.Dialog.__init__(self, parent, wx.ID_ANY, 'Select Version', style=style)
+        pnl = wx.Panel(self)
+        sizer = wx.BoxSizer(wx.VERTICAL)
+        insver = GSASIIpath.svnGetRev(local=True)
+        curver = int(GSASIIpath.svnGetRev(local=False))
+        label = wx.StaticText(
+            pnl,  wx.ID_ANY,
+            'Select a specific GSAS-II version to install'
+            )
+        sizer.Add(label, 0, wx.ALIGN_CENTRE|wx.ALL, 5)
+        sizer1 = wx.BoxSizer(wx.HORIZONTAL)
+        sizer1.Add(
+            wx.StaticText(pnl,  wx.ID_ANY,
+                          'Currently installed version: '+str(insver)),
+            0, wx.ALIGN_CENTRE|wx.ALL, 5)
+        sizer.Add(sizer1)
+        sizer1 = wx.BoxSizer(wx.HORIZONTAL)
+        sizer1.Add(
+            wx.StaticText(pnl,  wx.ID_ANY,
+                          'Select GSAS-II version to install: '),
+            0, wx.ALIGN_CENTRE|wx.ALL, 5)
+        self.spin = wx.SpinCtrl(pnl, wx.ID_ANY)
+        self.spin.SetRange(1, curver)
+        self.spin.SetValue(curver)
+        self.Bind(wx.EVT_SPINCTRL, self._onSpin, self.spin)
+        self.Bind(wx.EVT_KILL_FOCUS, self._onSpin, self.spin)
+        sizer1.Add(self.spin)
+        sizer.Add(sizer1)
+
+        line = wx.StaticLine(pnl,-1, size=(-1,3), style=wx.LI_HORIZONTAL)
+        sizer.Add(line, 0, wx.EXPAND|wx.ALIGN_CENTER|wx.ALL, 10)
+
+        self.text = wx.StaticText(pnl,  wx.ID_ANY, "")
+        sizer.Add(self.text, 0, wx.ALIGN_LEFT, 5)
+
+        btnsizer = wx.StdDialogButtonSizer()
+        btn = wx.Button(pnl, wx.ID_OK, "Install")
+        btn.SetDefault()
+        btnsizer.AddButton(btn)
+        btn = wx.Button(pnl, wx.ID_CANCEL)
+        btnsizer.AddButton(btn)
+        btnsizer.Realize()
+        sizer.Add(btnsizer, 0, wx.ALIGN_CENTER|wx.ALL, 5)
+        pnl.SetSizer(sizer)
+        sizer.Fit(self)
+        self.topsizer=sizer
+        self.CenterOnParent()
+        self._onSpin(None)
+
+    def _onSpin(self,event):
+        'Called to load info about the selected version in the dialog'
+        ver = self.spin.GetValue()
+        d = GSASIIpath.svnGetLog(version=ver)
+        date = d.get('date','?').split('T')[0]
+        s = '(Version '+str(ver)+' created '+date
+        s += ' by '+d.get('author','?')+')'
+        msg = d.get('msg')
+        if msg: s += '\n\nComment: '+msg
+        self.text.SetLabel(s)
+        self.topsizer.Fit(self)
+
+    def getVersion(self):
+        'Get the version number in the dialog'
+        return self.spin.GetValue()
+
+################################################################################
 class MyHelp(wx.Menu):
     '''
@@ -1181 +1252 @@
                 text='&Check for updates')
             frame.Bind(wx.EVT_MENU, self.OnCheckUpdates, helpobj)
+            helpobj = self.Append(
+                help='', id=wx.ID_ANY, kind=wx.ITEM_NORMAL,
+                text='&Regress to an old GSAS-II version')
+            frame.Bind(wx.EVT_MENU, self.OnSelectVersion, helpobj)
         for lbl,indx in morehelpitems:
             helpobj = self.Append(text=lbl,
@@ -1268 +1343 @@
                                    'You have version '+local+
                                    ' of GSAS-II installed, but the current version is '+repos+
-                                   '. However, you have modified '+str(len(mods))+
+                                   '. However, '+str(len(mods))+
                                    ' file(s) on your local computer have been modified.'
-                                   ' Updating could wipe out your local changes. Press OK to start an update:',
+                                   ' Updating could cause you to lose your changes, if conflicts arise. Press OK to start an update if this is acceptable:',
                                    'Local GSAS-II Mods',
                                    wx.OK|wx.CANCEL)
@@ -1294 +1369 @@
             dlg.ShowModal()
             return
-        modsbytype = {}
-        for key in moddict:
-            typ = moddict[key]
-            if modsbytype.get(typ) is None:
-                modsbytype[typ] = []
-            modsbytype[typ].append(key)
-        msg = 'Update was completed. Changes will take effect when GSAS-II is next updated. The following files were updated, ordered by status:'
-        for key in modsbytype:
-            msg += '\n' + key + ':\n\t'
-            for fil in modsbytype:
-                msg += fil + ', '
+        msg = 'Update was completed. Changes will take effect when GSAS-II is restarted.\n\nThe following files were affected, ordered by change,'
+        for key in sorted(moddict.keys()):
+            msg += '\n\n' + key + ': '+moddict[key]
+        dlg = wx.MessageDialog(self.frame,msg, 'Update Completed', wx.OK)
+        dlg.ShowModal()
+        return
+
+    def OnSelectVersion(self,event):
+        '''Allow the user to select a specific version of GSAS-II
+        '''
+        if not GSASIIpath.whichsvn():
+            dlg = wx.MessageDialog(self,'No Subversion','Cannot update GSAS-II because subversion (svn) '+
+                                   'was not found.'
+                                   ,wx.OK)
+            dlg.ShowModal()
+            return
+        local = GSASIIpath.svnGetRev()
+        if local is None: 
+            dlg = wx.MessageDialog(self.frame,
+                                   'Unable to run subversion on the GSAS-II current directory. Is GSAS-II installed correctly?',
+                                   'Subversion error',
+                                   wx.OK)
+            dlg.ShowModal()
+            return
+        mods = GSASIIpath.svnFindLocalChanges()
+        if mods:
+            dlg = wx.MessageDialog(self.frame,
+                                   'You have version '+local+
+                                   ' of GSAS-II installed. However, '+str(len(mods))+
+                                   ' file(s) on your local computer have been modified.'
+                                   ' Downdating is not encouraged as this could cause you to lose these changes. Press OK to continue anyway:',
+                                   'Local GSAS-II Mods',
+                                   wx.OK|wx.CANCEL)
+            if dlg.ShowModal() != wx.ID_OK: return
+        dlg = downdate(parent=self.frame)
+        if dlg.ShowModal() == wx.ID_OK:
+            ver = dlg.getVersion()
+            print('start update to '+str(ver))
+            wx.BeginBusyCursor()
+            moddict = GSASIIpath.svnUpdateDir(version=ver)
+            wx.EndBusyCursor()
+            dlg.Destroy()
+        else:
+            dlg.Destroy()
+            return
+        if moddict is None: 
+            dlg = wx.MessageDialog(self.frame,
+                                   'Error accessing the GSAS-II server or performing the update. '+
+                                   'Try again later or perform a manual update',
+                                   'Update Error',
+                                   wx.OK)
+            dlg.ShowModal()
+            return
+        msg = 'Update was completed. Changes will take effect when GSAS-II is restarted.\n\nThe following files were affected, ordered by change,'
+        for key in sorted(moddict.keys()):
+            msg += '\n\n' + key + ': '+moddict[key]
         dlg = wx.MessageDialog(self.frame,msg, 'Update Completed', wx.OK)
         dlg.ShowModal()

trunk/GSASIImath.py

@@ -1281 +1281 @@
         esdoff = 5
     valoff = 0
-    if esdoff < 0 or abs(value) > 1.0e6 or abs(value) < 1.0e-4: # use scientific notation
+    if abs(value) < abs(esdoff): # value is effectively zero
+        pass
+    elif esdoff < 0 or abs(value) > 1.0e6 or abs(value) < 1.0e-4: # use scientific notation
         # where the digit offset is to the left of the decimal place or where too many
         # digits are needed
@@ -1297 +1299 @@
         extra = -math.log10(abs(value))
         if extra > 0: extra += 1
+        print 'fmt=',"{:."+str(max(0,esdoff+int(extra)))+"f}"
         out = ("{:."+str(max(0,esdoff+int(extra)))+"f}").format(value) # format the value
     if esd > 0:

trunk/GSASIIobj.py

@@ -125 +125 @@
 =============  ===============  ====================================================
 
-Phase Tree Item
+Phase Tree Items
 ----------------
 
@@ -272 +272 @@
             Asymmetric unit coordinates [X is (x,y,z)]
             are transformed using
-            :math:`X\prime = M_n*X+T_n`
+            :math:`X^\prime = M_n*X+T_n`
 SGSys       symmetry unit cell: type one of
             'triclinic', 'monoclinic', 'orthorhombic',
@@ -315 +315 @@
 cia+2...cia+6     U11, U22, U33, U12, U13, U23
 ==============   ====================================================
+
+Powder Diffraction Tree Items
+-----------------------------
+
+.. _Powder_table:
+
+.. index::
+   single: Powder data object description
+   single: Data object descriptions; Powder Data
+
+Every powder diffraction histogram is stored in the GSAS-II data tree
+with a top-level entry named beginning with the string "PWDR ". The
+diffraction data for that information are directly associated with
+that tree item and there are a series of children to that item. The
+routine :func:`~GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree` will
+load this information into a dictionary where the child tree name is
+used as a key, and the information in the main entry is assigned
+a key of ``Data``, as outlined below.
+
+.. tabularcolumns:: |l|l|p{4in}|
+
+======================  ===============  ====================================================
+  key                      sub-key        explanation
+======================  ===============  ====================================================
+Limits                       \            A list of two two element lists, as [[Ld,Hd],[L,H]]
+                                          where L and Ld are the current and default lowest
+                                          two-theta value to be used and 
+                                          where H and Hd are the current and default highest
+                                          two-theta value to be used.
+Reflection Lists              \           A dict with an entry for each phase in the
+                                          histogram. The contents of each dict item
+                                          is a list or reflections as described in the
+                                          :ref:`Powder Reflections <PowderRefl_table>`
+                                          description.
+Instrument Parameters         \           A list containing two dicts where the possible
+                                          keys in each dict are listed below. The value
+                                          for each item is a list containing three values:
+                                          the initial value, the current value and a
+                                          refinement flag which can have a value of
+                                          True, False or 0 where 0 indicates a value that
+                                          cannot be refined. The first and second
+                                          values are floats unless otherwise noted.
+                                          Items in the first dict are noted as [1]
+\                         Lam             Specifies a wavelength in Angstroms [1]
+\                         Lam1            Specifies the primary wavelength in
+                                          Angstrom, when an alpha1, alpha2
+                                          source is used [1]
+\                         Lam2            Specifies the secondary wavelength in
+                                          Angstrom, when an alpha1, alpha2
+                                          source is used [1]
+                          I(L2)/I(L1)     Ratio of Lam2 to Lam1 [1]           
+\                         Type            Histogram type (str) [1]: 
+                                           * 'PXC' for constant wavelength x-ray
+                                           * 'PNC' for constant wavelength neutron
+                                           * 'PNT' for time of flight neutron
+\                         Zero            Two-theta zero correction in *degrees* [1]
+\                         Azimuth         Azimuthal setting angle for data recorded
+                                          with differing setting angles [1]
+\                         U, V, W         Cagliotti profile coefficients
+                                          for Gaussian instrumental broadening, where the
+                                          FWHM goes as
+                                          :math:`U \\tan^2\\theta + V \\tan\\theta + W` [1]
+\                         X, Y            Cauchy (Lorentzian) instrumental broadening
+                                          coefficients [1]
+\                         SH/L            Variant of the Finger-Cox-Jephcoat asymmetric
+                                          peak broadening ratio. Note that this is the
+                                          average between S/L and H/L where S is
+                                          sample height, H is the slit height and
+                                          L is the goniometer diameter. [1]
+\                         Polariz.        Polarization coefficient. [1]
+wtFactor                      \           A weighting factor to increase or decrease
+                                          the leverage of data in the histogram (float).
+                                          A value of 1.0 weights the data with their
+                                          standard uncertainties and a larger value
+                                          increases the weighting of the data (equivalent
+                                          to decreasing the uncertainties).
+Sample Parameters             \           Specifies a dict with parameters that describe how
+                                          the data were collected, as listed
+                                          below. Refinable parameters are a list containing
+                                          a float and a bool, where the second value
+                                          specifies if the value is refined, otherwise
+                                          the value is a float unless otherwise noted.
+\                         Scale           The histogram scale factor (refinable) 
+\                         Absorption      The sample absorption coefficient as
+                                          :math:`\\mu r` where r is the radius
+                                          (refinable).
+\                         DisplaceX,      Sample displacement from goniometer center
+                          DisplaceY       where Y is along the beam direction and
+                                          X is perpendicular. Units are :math:`\\mu m`
+                                          (refinable).
+\                         Phi, Chi,       Goniometer sample setting angles, in degrees.
+                          Omega
+\                         Gonio. radius   Radius of the diffractometer in mm
+\                         InstrName       A name for the instrument, used in preparing
+                                          a CIF (str).
+\                         Force,          Variables that describe how the measurement
+                          Temperature,    was performed. Not used directly in 
+                          Humidity,       any computations. 
+                          Pressure,
+                          Voltage
+\                         ranId           The random-number Id for the histogram
+                                          (same value as where top-level key is ranId)
+\                         Type            Type of diffraction data, may be 'Debye-Scherrer'
+                                          or 'Bragg-Brentano' (str).
+\                         Diffuse         not in use?
+hId                           \           The number assigned to the histogram when
+                                          the project is loaded or edited (can change)
+ranId                         \           A random number id for the histogram
+                                          that does not change
+Background                    \           The background is stored as a list with where
+                                          the first item in the list is list and the second
+                                          item is a dict. The list contains the background
+                                          function and its coefficients; the dict contains
+                                          Debye diffuse terms and background peaks.
+                                          (TODO: this needs to be expanded.)
+Data                          \           The data consist of a list of 6 np.arrays 
+                                          containing in order:
+
+                                           1. the x-postions (two-theta in degrees),
+                                           2. the intensity values (Yobs),
+                                           3. the weights for each Yobs value
+                                           4. the computed intensity values (Ycalc)
+                                           5. the background values
+                                           6. Yobs-Ycalc
+======================  ===============  ====================================================
+
+Powder Reflection Data Structure
+--------------------------------
+
+.. _PowderRefl_table:
+
+.. index::
+   single: Powder reflection object description
+   single: Data object descriptions; Powder Reflections
+   
+For every phase in a histogram, the ``Reflection Lists`` value is a list of
+reflections. The items in that list are documented below.
+
+==========  ====================================================
+  index         explanation
+==========  ====================================================
+ 0,1,2       h,k,l (float)
+ 3           multiplicity
+ 4           d-space, Angstrom
+ 5           pos, two-theta
+ 6           sig, Gaussian width
+ 7           gam, Lorenzian width
+ 8           Fobs**2
+ 9           Fcalc**2
+ 10          reflection phase, in degrees
+ 11          the equivalent reflections as a (m x 3) 
+             np.array, where m is 0.5 * multiplicity. Note
+             that Freidel pairs, (-h,-k-,l), are not
+             included. 
+ 12          phase shift for each of the equivalent
+             reflections as a length (m) array
+ 13          intensity correction for reflection, this times
+             Fobs**2 or Fcalc**2 gives Iobs or Icalc 
+ 14          dict with the form factor (f or b) by atom type
+             symbol at the reflection position.
+==========  ====================================================
 
 

trunk/GSASIIpath.py

@@ -80 +80 @@
     "svn/bin" in the location of the GSASII source files.
 
-    :returns: None if svn is not found.
+    :returns: None if svn is not found or an absolute path to the subversion
+    executable file .
     '''
     def is_exe(fpath):
@@ -92 +93 @@
         exe_file = os.path.join(path, svnprog)
         if is_exe(exe_file):
-            return exe_file
+            return os.path.abspath(exe_file)
+
+def svnGetLog(fpath=os.path.split(__file__)[0],version=None):
+    '''Get the revision log information for a specific version of the 
+
+    :param str fpath: path to repository dictionary, defaults to directory where
+       the current file is located.
+    :param int version: the version number to be looked up or None (default)
+       for the latest version.
+
+    :returns: a dictionary with keys (one hopes) 'author', 'date', 'msg', and 'revision'
+
+    '''
+    import subprocess
+    import xml.etree.ElementTree as ET
+    svn = whichsvn()
+    if not svn: return
+    if version is not None:
+        vstr = '-r'+str(version)
+    else:
+        vstr = '-rHEAD'
+
+    cmd = [svn,'log',fpath,'--xml',vstr]
+    s = subprocess.Popen(cmd,
+                         stdout=subprocess.PIPE,stderr=subprocess.PIPE)
+    out,err = s.communicate()
+    if err:
+        print 'out=',out
+        print 'err=',err
+        return None
+    x = ET.fromstring(out)
+    d = {}
+    for i in x.iter('logentry'):
+        d = {'revision':i.attrib.get('revision','?')}
+        for j in i:
+            d[j.tag] = j.text
+        break # only need the first
+    return d
 
 def svnGetRev(fpath=os.path.split(__file__)[0],local=True):
-    '''This obtains the version number for the either the latest local last update
+    '''Obtain the version number for the either the last update of the local version
     or contacts the subversion server to get the latest update version (# of Head).
 
-    :param fpath: path to repository dictionary, defaults to directory where
+    :param str fpath: path to repository dictionary, defaults to directory where
        the current file is located
-    :param local: determines the type of version number, where
+    :param bool local: determines the type of version number, where
        True (default): returns the latest installed update 
        False: returns the version number of Head on the server
@@ -155 +193 @@
     return changed
 
-def svnUpdateDir(fpath=os.path.split(__file__)[0]):
+def svnUpdateDir(fpath=os.path.split(__file__)[0],version=None):
     '''This performs an update of the files in a local directory from a server. 
 
@@ -172 +210 @@
     svn = whichsvn()
     if not svn: return
-    cmd = [svn,'update',fpath,'-rHEAD',
+    if version:
+        verstr = '-r' + str(version)
+    else:
+        verstr = '-rHEAD'
+    cmd = [svn,'update',fpath,verstr,
            '--non-interactive',
            '--accept','theirs-conflict','--force']
@@ -178 +220 @@
                          stdout=subprocess.PIPE,stderr=subprocess.PIPE)
     out,err = s.communicate()
-    if err: return
+    print out
+    if err:
+        print err
+        return
     l = out.split()
     updates = {}
@@ -186 +231 @@
         t = changetype.get(i[0])
         if not t: continue
-        updates[j] = t
+        f = os.path.split(j)[1]
+        if updates.get(t):
+            updates[t] += ', '+f
+        else:
+            updates[t] = f
     return updates

trunk/GSASIIstrIO.py

@@ -1514 +1514 @@
 ################################################################################        
                     
-def GetHistogramPhaseData(Phases,Histograms,Print=True,pFile=None):
-    'needs a doc string'
+def GetHistogramPhaseData(Phases,Histograms,Print=True,pFile=None,resetRefList=True):
+    '''Loads the HAP histogram/phase information into dicts
+
+    :param dict Phases: phase information
+    :param dict Histograms: Histogram information
+    :param bool Print: prints information as it is read
+    :param file pFile: file object to print to (the default, None causes printing to the console)
+    :param bool resetRefList: Should the contents of the Reflection List be initialized
+      on loading. The default, True, initializes the Reflection List as it is loaded.
+
+    :returns: (hapVary,hapDict,controlDict)
+      * hapVary: list of refined variables
+      * hapDict: dict with refined variables and their values
+      * controlDict: dict with computation controls (?)
+    '''
     
     def PrintSize(hapData):
@@ -1722 +1735 @@
                     else:
                         raise ValueError 
-                Histogram['Reflection Lists'][phase] = refList
+                if resetRefList: Histogram['Reflection Lists'][phase] = refList
             elif 'HKLF' in histogram:
                 inst = Histogram['Instrument Parameters'][0]

trunk/exports/G2cif.py

@@ -13 +13 @@
 import GSASIIlattice as G2lat
 import GSASIIspc as G2spg
-reload(G2spg)
+#reload(G2spg)
+reload(G2mth)
 
 def getCallerDocString(): # for development
@@ -39 +40 @@
           "simple" for a simple CIF with only coordinates
         '''
+    
         def WriteCIFitem(name,value=''):
             if value:
@@ -571 +573 @@
                 WriteDistances(phasenam,SymOpList,offsetList,symOpList,G2oprList)
 
-            #raise Exception,'Testing'
-
         def WritePowderData(histlbl):
             text = '?'
             histblk = self.Histograms[histlbl]
+            inst = histblk['Instrument Parameters'][0]
+            hId = histblk['hId']
+            pfx = ':' + str(hId) + ':'
             print 'TODO: powder here data for',histblk["Sample Parameters"]['InstrName']
             # see wrpowdhist.for & wrreflist.for
             
-            refprx = '_refln.' # mm
+            #refprx = '_refln.' # mm
             refprx = '_refln_' # normal
+
+            print histblk.keys()
+            #            for key in histblk:
+            #                print key
+            print inst
+            print self.parmDict.keys()
+            print self.sigDict.keys()
+            WriteCIFitem('\n# SCATTERING FACTOR INFO')
+            if 'Lam1' in inst:
+                ratio = self.parmDict.get('I(L2)/I(L1)',inst['I(L2)/I(L1)'][1])
+                sratio = self.sigDict.get('I(L2)/I(L1)',-0.0009)
+                lam1 = self.parmDict.get('Lam1',inst['Lam1'][1])
+                slam1 = self.sigDict.get('Lam1',-0.00009)
+                lam2 = self.parmDict.get('Lam2',inst['Lam2'][1])
+                slam2 = self.sigDict.get('Lam2',-0.00009)
+                # always assume Ka1 & Ka2 if two wavelengths are present
+                WriteCIFitem('loop_' + 
+                             '\n\t_diffrn_radiation_wavelength' +
+                             '\n\t_diffrn_radiation_wavelength_wt' + 
+                             '\n\t_diffrn_radiation_type' + 
+                             '\n\t_diffrn_radiation_wavelength_id')
+                WriteCIFitem('  ' + PutInCol(G2mth.ValEsd(lam1,slam1),15)+
+                             PutInCol('1.0',15) + 
+                             PutInCol('K\\a~1~',10) + 
+                             PutInCol('1',5))
+                WriteCIFitem('  ' + PutInCol(G2mth.ValEsd(lam2,slam2),15)+
+                             PutInCol(G2mth.ValEsd(ratio,sratio),15)+
+                             PutInCol('K\\a~2~',10) + 
+                             PutInCol('2',5))                
+            else:
+                lam1 = self.parmDict.get('Lam',inst['Lam'])
+                slam1 = self.sigDict.get('Lam',-0.00009)
+                WriteCIFitem('_diffrn_radiation_wavelength',G2mth.ValEsd(lam1,slam1))
+
+            raise Exception, "testing"
 
             if not oneblock:
@@ -593 +631 @@
                     for phasenam in phasebyhistDict.get(histlbl):
                         pass
-
-            WriteCIFitem('\n# SCATTERING FACTOR INFO')
-            WriteCIFitem('_diffrn_radiation_wavelength' ,text)
-            #WriteCIFitem('_diffrn_radiation_type',text)
-            #C always assume Ka1 & Ka2 if two wavelengths are present
-            #WriteCIFitem('loop_' + 
-            #             '\n\t_diffrn_radiation_wavelength' +
-            #             '\n\t_diffrn_radiation_wavelength_wt' + 
-            #             '\n\t_diffrn_radiation_type' + 
-            #             '\n\t_diffrn_radiation_wavelength_id')
-            #WRITE LAM1,1.0,'K\\a~1~',1, LAM2,ratio,'K\\a~2~',2
 
             WriteCIFitem('_pd_proc_ls_prof_R_factor','?')
@@ -642 +669 @@
                 # instrumental profile terms go here
                 WriteCIFitem('_pd_proc_ls_profile_function','?')
+
+            #print 'Data'
+            #for item in histblk['Data']:
+            #    print item
+                #try:
+                #    print key,histblk[key].keys()
+                #except:
+                #    print key
+                #    print histblk[key]
+            #print 'Background'
+            print histblk['Reflection Lists']['Garnet'][1]
+            for i in range(0,80):
+                for j in [0,1,2,13]:
+                    print histblk['Reflection Lists']['Garnet'][i][j],
+                print
+                #print histblk['Reflection Lists']['Garnet'][i][12].shape
+                #print histblk['Reflection Lists']['Garnet'][i][14]
+            #print histblk['Background'][0]
+            #print histblk['Background'][1]
+            import numpy as np
+            refList = np.array([refl[:11] for refl in histblk['Reflection Lists']['Garnet']])
+            #refList = histblk['Reflection Lists']['Garnet']
+            Icorr = np.array([refl[13] for refl in histblk['Reflection Lists']['Garnet']])
+            FO2 = np.array([refl[8] for refl in histblk['Reflection Lists']['Garnet']])
+            print Icorr
+            I100 = refList.T[8]*Icorr
+            print I100
+            print I100/max(I100)
+            Icorr = np.array([refl[13] for refl in histblk['Reflection Lists']['Garnet']]) * np.array([refl[8] for refl in histblk['Reflection Lists']['Garnet']])
+            print I100/max(I100)
 
             WriteCIFitem('\n# STRUCTURE FACTOR TABLE')            
@@ -733 +790 @@
         #============================================================
         # the export process starts here
-        # create a dict with refined values and their uncertainties
-        self.loadParmDict()
         # also load all of the tree into a set of dicts
         self.loadTree()
         #self.dumpTree()
+        # create a dict with refined values and their uncertainties
+        self.loadParmDict()
+        #
 
         # get restraint info
@@ -881 +939 @@
                 WritePubTemplate()
                 WriteOverall()
+                WritePhaseTemplate()
             # report the phase info
-            WritePhaseTemplate()
             WritePhaseInfo(phasenam)
             if hist.startswith("PWDR") and not self.quickmode: