Changeset 3806


Ignore:
Timestamp:
Jan 30, 2019 5:15:41 PM (3 years ago)
Author:
toby
Message:

redo parameter lookup to provide numerical deriv step size (see G2obj.getVarStep)

Location:
trunk
Files:
4 edited

Legend:

Unmodified
Added
Removed

  • trunk/GSASIIIO.py

    r3772 r3806  
    576576   
    577577def objectScan(data,tag,indexStack=[]):
    578     '''Scan an object looking for unexpected data types'''
     578    '''Recursively scan an object looking for unexpected data types.
     579    This is used in debug mode to scan .gpx files for objects we did not
     580    intend to be there.
     581    '''
    579582    if type(data) is list or type(data) is tuple:
    580583        for i in range(len(data)):

  • trunk/GSASIIdataGUI.py

    r3805 r3806  
    45454545            try:
    45464546                if dlg2.ShowModal() == wx.ID_OK:
    4547                     self.GPXtree.DeleteChildren(self.root)
    4548                     self.HKL = []
    4549                     G2IO.ProjFileOpen(self,False)
    4550                     self.TreeItemDelete = False  # tree has been repopulated; ignore previous deletions
    4551                     self.GPXtree.RestoreExposedItems() # reset exposed/hidden tree items       
    4552                     self.ResetPlots()
     4547                    wx.CallAfter(self.reloadFromGPX)
    45534548            finally:
    45544549                dlg2.Destroy()
    45554550        else:
    45564551            self.ErrorDialog('Refinement error',Msg)
     4552
     4553    def reloadFromGPX(self):
     4554        '''Deletes current data tree & reloads it from GPX file (after a
     4555        refinemnt.) Done after events are completed to avoid crashes.
     4556        '''
     4557        self.GPXtree.DeleteChildren(self.root)
     4558        self.HKL = []
     4559        G2IO.ProjFileOpen(self,False)
     4560        self.TreeItemDelete = False  # tree has been repopulated; ignore previous deletions
     4561        self.GPXtree.RestoreExposedItems() # reset exposed/hidden tree items
     4562        self.ResetPlots()       
    45574563       
    45584564    def SaveTreeSetting(self):

  • trunk/GSASIIobj.py

    r3802 r3806  
    10121012'''
    10131013
    1014 VarDesc = {}
    1015 ''' This dictionary lists descriptions for GSAS-II variables,
    1016 as set in :func:`CompileVarDesc`. See that function for a description
    1017 for how keys and values are written.
     1014#VarDesc = {}  # removed 1/30/19 BHT as no longer needed (I think)
     1015#''' This dictionary lists descriptions for GSAS-II variables,
     1016#as set in :func:`CompileVarDesc`. See that function for a description
     1017#for how keys and values are written.
     1018#'''
     1019
     1020reVarDesc = {}
     1021''' This dictionary lists descriptions for GSAS-II variables where
     1022keys are compiled regular expressions that will match the name portion
     1023of a parameter name. Initialized in :func:`CompileVarDesc`.
    10181024'''
    10191025
    1020 reVarDesc = {}
    1021 ''' This dictionary lists descriptions for GSAS-II variables with
    1022 the same values as :attr:`VarDesc` except that keys have been compiled as
    1023 regular expressions. Initialized in :func:`CompileVarDesc`.
     1026reVarStep = {}
     1027''' This dictionary lists the preferred step size for numerical
     1028derivative computation w/r to a GSAS-II variable. Keys are compiled
     1029regular expressions and values are the step size for that parameter.
     1030Initialized in :func:`CompileVarDesc`.
    10241031'''
    10251032# create a default space group object for P1; N.B. fails when building documentation
    … …  
    13091316    '''
    13101317
    1311     # special handling for parameter names without a colons
     1318    # special handling for parameter names without a colon
    13121319    # for now, assume self-defining
    13131320    if varname.find(':') == -1:
    … …  
    14121419
    14131420def CompileVarDesc():
    1414     '''Set the values in the variable description lookup table (:attr:`VarDesc`)
    1415     into :attr:`reVarDesc`. This is called in :func:`getDescr` so the initialization
    1416     is always done before use.
     1421    '''Set the values in the variable lookup tables
     1422    (:attr:`reVarDesc` and :attr:`reVarStep`).
     1423    This is called in :func:`getDescr` and :func:`getVarStep` so this
     1424    initialization is always done before use.
    14171425
    14181426    Note that keys may contain regular expressions, where '[xyz]'
    1419     matches 'x' 'y' or 'z' (equivalently '[x-z]' describes this as range of values).
    1420     '.*' matches any string. For example::
     1427    matches 'x' 'y' or 'z' (equivalently '[x-z]' describes this as range
     1428    of values). '.*' matches any string. For example::
    14211429
    14221430    'AUiso':'Atomic isotropic displacement parameter',
    … …  
    14421450        'Scale' : 'Phase or Histogram scale factor',
    14431451        # Phase vars (p::<var>)
    1444         'A([0-5])' : 'Reciprocal metric tensor component \\1',
     1452        'A([0-5])' : ('Reciprocal metric tensor component \\1',1e-5),
    14451453        '[vV]ol' : 'Unit cell volume', # probably an error that both upper and lower case are used
    14461454        # Atom vars (p::<var>:a)
    1447         'dA([xyz])$' : 'change to atomic coordinate, \\1',
     1455        'dA([xyz])$' : ('change to atomic coordinate, \\1',1e-6),
    14481456        'A([xyz])$' : '\\1 fractional atomic coordinate',
    1449         'AUiso':'Atomic isotropic displacement parameter',
    1450         'AU([123][123])':'Atomic anisotropic displacement parameter U\\1',
    1451         'Afrac': 'Atomic site fraction parameter',
     1457        'AUiso':('Atomic isotropic displacement parameter',1e-4),
     1458        'AU([123][123])':('Atomic anisotropic displacement parameter U\\1',1e-4),
     1459        'Afrac': ('Atomic site fraction parameter',1e-5),
    14521460        'Amul': 'Atomic site multiplicity value',
    14531461        'AM([xyz])$' : 'Atomic magnetic moment parameter, \\1',
    … …  
    14721480        #Histogram vars (:h:<var>)
    14731481        'Absorption' : 'Absorption coef.',
    1474         'Displace([XY])' : 'Debye-Scherrer sample displacement \\1',
    1475         'Lam' : 'Wavelength',
    1476         'I\(L2\)\/I\(L1\)' : 'Ka2/Ka1 intensity ratio',
    1477         'Polariz\.' : 'Polarization correction',
    1478         'SH/L' : 'FCJ peak asymmetry correction',
    1479         '([UVW])$' : 'Gaussian instrument broadening \\1',
    1480         '([XYZ])$' : 'Cauchy instrument broadening \\1',
     1482        'Displace([XY])' : ('Debye-Scherrer sample displacement \\1',0.1),
     1483        'Lam' : ('Wavelength',1e-6),
     1484        'I\(L2\)\/I\(L1\)' : ('Ka2/Ka1 intensity ratio',0.001),
     1485        'Polariz\.' : ('Polarization correction',1e-3),
     1486        'SH/L' : ('FCJ peak asymmetry correction',1e-4),
     1487        '([UVW])$' : ('Gaussian instrument broadening \\1',1e-5),
     1488        '([XYZ])$' : ('Cauchy instrument broadening \\1',1e-5),
    14811489        'Zero' : 'Debye-Scherrer zero correction',
    14821490        'Shift' : 'Bragg-Brentano sample displ.',
    … …  
    15501558        'C\([0-9]*,[0-9]*\)' : 'spherical harmonics preferred orientation coef.',
    15511559        }.items():
    1552         VarDesc[key] = value
    1553         reVarDesc[re.compile(key)] = value
     1560        if len(value) == 2:
     1561            #VarDesc[key] = value[0]
     1562            reVarDesc[re.compile(key)] = value[0]
     1563            reVarStep[re.compile(key)] = value[1]
     1564        else:
     1565            #VarDesc[key] = value
     1566            reVarDesc[re.compile(key)] = value
    15541567
    15551568def removeNonRefined(parmList):
    … …  
    15861599            return m.expand(reVarDesc[key])
    15871600    return None
     1601
     1602def getVarStep(name,parmDict=None):
     1603    '''Return a step size for computing the derivative of a GSAS-II variable
     1604
     1605    :param str name: A complete variable name (with colons, :)
     1606    :param dict parmDict: A dict with parameter values or None (default)
     1607
     1608    :returns: a float that should be an appropriate step size, either from
     1609      the value supplied in :func:`CompileVarDesc` or based on the value for
     1610      name in parmDict, if supplied. If not found or the value is zero,
     1611      a default value of 1e-5 is used. If parmDict is None (default) and
     1612      no value is provided in :func:`CompileVarDesc`, then None is returned.
     1613    '''
     1614    CompileVarDesc() # compile the regular expressions, if needed
     1615    for key in reVarStep:
     1616        m = key.match(name)
     1617        if m:
     1618            return reVarStep[key]
     1619    if parmDict is None: return None
     1620    val = parmDict.get(key,0.0)
     1621    if abs(val) > 0.05:
     1622        return abs(val)/1000.
     1623    else:
     1624        return 1e-5
    15881625
    15891626def GenWildCard(varlist):
    … …  
    27442781        print (70*'*')
    27452782
     2783# Note that this is GUI code and should be moved at somepoint
    27462784def CreatePDFitems(G2frame,PWDRtree,ElList,Qlimits,numAtm=1,FltBkg=0,PDFnames=[]):
    27472785    '''Create and initialize a new set of PDF tree entries
    … …  
    28282866
    28292867if __name__ == "__main__":
     2868    # test variable descriptions
     2869    for var in '0::Afrac:*',':1:Scale','1::dAx:0','::undefined':
     2870        v = var.split(':')[2]
     2871        print(var+':\t', getDescr(v),getVarStep(v))
     2872    import sys; sys.exit()
    28302873    # test equation evaluation
    28312874    def showEQ(calcobj):

  • trunk/GSASIIstrMath.py

    r3805 r3806  
    486486            stepDict = {}
    487487            for parm in varyList:
    488                 if parm.split(':')[2].startswith('dA'):
    489                     stepDict[parm] = 1e-5
    490                 elif True:
    491                     stepDict[parm] = 1e-4
     488                stepDict[parm] = G2obj.getVarStep(parm,parmDict)
    492489            break
    493490    for phase in Phases:
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