Ticket #6863: t6863_cal.py

File t6863_cal.py, 9.1 KB (added by Wenduo Zhou, 7 years ago)
Line 
1######################################################################
2#
3# This is a partial copy from LeBailFitScript.py
4#
5# Python Script as Step 1 of Le Bail Fitting to
6# 1. Load file
7# 2. Create LeBailFitInput
8# 3. Fit Peaks
9#
10# Step 1:   Load data, model (HKL list) and starting instrument parameters values,
11#           and do an initial LeBailFit/calculation to see how much the starting
12#           values are off;
13
14#|-------------------------------------------------------------------------------------------
15#|Step 2.1: Fit single peaks for TOF_h, Alpha, Beta, and Sigma;
16#|
17#|Step 2.2: Plot parameters (TOF_H, Alpha, Beta and Sigma) against d-spacing;
18#|
19#|Step 2.3: Remove the peaks with bad fit;
20#|
21#|Step 2.4: Refine instrument geometry parameters;
22#|
23#|          It is possible to loop back to Step 2 to include more peaks with single peaks
24#|-------------------------------------------------------------------------------------------
25#
26# Step 5: Do Le Bail Fit from previous result to see whether the peak parameters are
27#         close enough for Le Bail Fit
28#
29# !Step 6: Fit Alpha, Beta and apply the change to
30#
31# !Step 7: Save the result files to HDD for Step 6, LeBailFit in random walk;
32#
33# Step 8: Save the result files to HDD for Step 6, LeBailFit in random walk;
34#
35# Step 7: Not in this script;
36#
37# Step 8: Process Monte Carlo results from Step 6
38#
39#
40######################################################################
41from Calibration_ImportInformation import *
42
43#--------------  Definition of Global Variables ---------------------
44bankid = 0
45
46datafilename = "" 
47hklfilename = ""
48irffilename = ""
49
50# montecarlofilename = ""
51# expirffilename = ""
52
53datawsname = ""
54instrparamwsname = ""
55braggpeakparamwsname = ""
56
57# outdataws1name = ""
58
59minpeakheight = 0.001
60
61# Range for Le Bail Fit of all peaks
62startx = -1
63endx =  -1
64# Range for fitting single peaks for step 1~3
65tofmin_singlepeaks = -1
66tofmax_singlepeaks = -1
67
68backgroundtype = "Polynomial"
69backgroundorder = 6
70bkgdtablewsname = ""
71bkgdwsname = ""
72bkgdfilename = ""
73usrbkgdpoints = ''
74
75latticesize = 4.1568899999999998
76#--------------------------------------------------------------------
77
78
79def setupGlobals(infofilename):
80    """ Set up globals values
81    """
82    global datafilename, hklfilename, irffilename 
83    global datawsname, instrparamwsname, braggpeakparamwsname
84    global bkgdtablewsname, bkgdwsname, bkgdfilename, backgroundorder
85    global tofmin_singlepeaks, tofmax_singlepeaks, startx, endx
86    global bankid, latticesize
87    global usrbkgdpoints
88
89    bankid, calibDict = importCalibrationInformation(infofilename)
90    bankid = int(bankid)
91
92    datafilename = calibDict["DataFileDir"] + calibDict[bankid]["DataFileName"] 
93    hklfilename  = calibDict["HKLFileDir"]  + calibDict[bankid]["HKLFileName"]
94    irffilename  = calibDict["IrfFileDir"]  + calibDict[bankid]["IrfFileName"]
95   
96    startx = float(calibDict[bankid]["LeBailFitMinTOF"])
97    endx   = float(calibDict[bankid]["LeBailFitMaxTOF"])
98
99    # Name of workspaces
100    datawsname = calibDict[bankid]["DataWorkspace"]
101    instrparamwsname     = "Bank%sInstrumentParameterTable" % (bankid)
102    braggpeakparamwsname = 'BraggPeakParameterTable'
103
104    # Background related
105    usrbkgdpoints   = calibDict[bankid]["UserSpecifiedBkgdPts"]
106    bkgdwsname      = datawsname+"_Background"
107    backgroundtype  = calibDict["BackgroundType"]
108    backgroundorder = int(calibDict["BackgroundOrder"])
109    bkgdfilename    = calibDict["WorkingDir"] + datawsname + "_Parameters.bak'"
110    bkgdwsname      = datawsname + "_Background"
111    bkgdtablewsname = datawsname + "_Background_Parameters"
112
113    # Other constants
114    latticesize   = calibDict[bankid]["LatticeSize"]
115
116    return
117
118#------------------------------------------------------------------------------
119# TableWorkspace Processing
120#------------------------------------------------------------------------------
121def parseRefineGeometryMCResultWorkspace(tablews):
122    """ Parse the refinement result workspac
123    """
124    numrows = tablews.rowCount()
125    numcols  = tablews.columnCount()
126    colnames = tablews.getColumnNames()
127
128    parameterdict = {}
129
130    for irow in xrange(numrows):
131        ppdict = {}
132        for icol in xrange(numcols):
133            colname = colnames[icol]
134            value = tablews.cell(irow, icol)
135            ppdict[colname] = value
136        # ENDFOR Column
137        chi2 = ppdict["Chi2"]
138
139        parameterdict[chi2] = ppdict
140    # ENDFOR
141
142    return parameterdict
143
144
145#def updateInstrumentParameterValue(tablews, paramdict):
146#    """ Update the value to an instrument parameter table
147#    """
148#    paramnames = paramdict.keys()
149#    for parname in paramnames:
150#        parvalue = paramdict[parname]
151#       # print "%s = %f" % (parname, parvalue)
152#       if parname.count("Chi2") == 0:
153#           # Only update parameters nothing to do with chi2
154#            UpdatePeakParameterTableValue(InputWorkspace=tablews,
155#               Column='Value',
156#                ParameterNames=[parname],
157#               NewFloatValue=parvalue)
158#
159#    return
160
161       
162def doStep3():
163    """ Step 3: to check whether the refinement result is good for low-d region
164    """
165    global startx, endx
166    global datawsname, instrparamwsname, braggpeakparamwsname
167    global bkgdtablewsname, bkgdwsname, backgroundtype, backgroundorder
168    global bankid
169    global usrbkgdpoints
170
171    # 1. Process background
172    bkgdwsname = datawsname+"_Background"
173    ProcessBackground(InputWorkspace=datawsname, 
174            OutputWorkspace=bkgdwsname, 
175            Options='SelectBackgroundPoints',
176            LowerBound=startx, 
177            UpperBound=endx, 
178            BackgroundType=backgroundtype,
179            BackgroundPoints=usrbkgdpoints,
180            NoiseTolerance='0.10000000000000001')
181
182    functionstr = "name=%s,n=%d" % (backgroundtype, backgroundorder)
183    for iborder in xrange(backgroundorder+1):
184        functionstr = "%s,A%d=%.5f" % (functionstr, iborder, 0.0)
185    print "Background function: %s" % (functionstr)
186
187    Fit(Function='name=Polynomial,n=6,A0=0.657699,A1=3.68433e-05,A2=-1.29638e-08,A3=1.16778e-12,A4=-4.71439e-17,A5=8.8499e-22,A6=-6.26573e-27',
188            InputWorkspace=bkgdwsname,
189            MaxIterations='1000',
190            Minimizer='Levenberg-MarquardtMD',
191            CreateOutput='1',
192            Output=bkgdwsname,
193            StartX=startx,
194            EndX=endx)
195
196    # 2. Do calculation
197    usemcresult = True
198    try:
199        bestmdws = mtd["BestMCResult1"]
200    except KeyError:
201        usemcresult = False
202
203    outwsname = datawsname + "_Calculated"
204    if usemcresult is True:
205        # Use MC N results
206        paramdict = parseRefineGeometryMCResultWorkspace(bestmtdws)
207
208        raise NotImplementedError("Case 1")
209
210        index = 0
211        maxoutput = 1
212        for chi2 in sorted(paramdict.keys()):
213            # 1. Update parameter values
214            updateInstrumentParameterValue(mtd["Bank%sInstrumentParameterTable1"%(bankid)], paramdict[chi2])
215           
216            print "Fit range: %f , %f" % (startx, endx)
217       
218            LeBailFit(InputWorkspace=datawsname,
219                OutputWorkspace=outwsname,
220                InputParameterWorkspace='Bank%dInstrumentParameterTable1'%(bankid),
221                OutputParameterWorkspace='Bank%dInstrumentParameterTable1_%d'%(bankid, index),
222                InputHKLWorkspace='BraggPeakParameterTable1',
223                OutputPeaksWorkspace='BraggPeakParameterTable2_%d'%(index),
224                Function='Calculation',                     
225                FitRegion                       = '%f, %f' % (startx, endx),
226                BackgroundType='Polynomial',
227                BackgroundParametersWorkspace=bkgdtablewsname, 
228                UseInputPeakHeights='0',
229                PeakRadius='8',
230                Minimizer='Levenberg-Marquardt')
231
232            print "Pattern %s:  Instrumental Geometry Chi^2 = %.5f" % ('CalculatedPattern%d'%(index), chi2)
233            index += 1
234            if index >= maxoutput:
235                break
236        # ENDFOR
237    else:
238        # Use Version 2 result
239       
240        # data from manually refinement
241        # for pair in [("Dtt1", 22529.600), ("Dtt1t", 22747.400), ("Zerot", 15.792320), ("Width", 1.1072)]:
242
243        # data from Jason's
244        # for pair in [("Dtt1", 22584.512), ("Dtt1t", 22604.852), ("Zerot", 11.317320), ("Width", 1.0521)]:
245
246        index = 0
247        print "Fit range: %f , %f" % (startx, endx)
248        LeBailFit(InputWorkspace=datawsname,
249            OutputWorkspace=outwsname,
250            InputParameterWorkspace='Bank1InstrumentParametersTable',
251            OutputParameterWorkspace='Bank%dInstrumentParameterTable1_%d'%(bankid, index),
252            InputHKLWorkspace='BraggPeakParameterTable1',
253            OutputPeaksWorkspace='BraggPeakParameterTable2_%d'%(index),
254            Function='Calculation',
255            FitRegion                       = '%f, %f' % (startx, endx),
256            BackgroundType='Polynomial',
257            BackgroundParametersWorkspace=bkgdtablewsname, 
258            UseInputPeakHeights='0',
259            PeakRadius='8',
260            Minimizer='Levenberg-Marquardt')
261
262    return
263
264def main(argv):
265    """ Main
266    """   
267    setupGlobals("Calibration_Information.config")
268   
269    print "Le Bail Fit Calibration Instrument... Step 3"
270    doStep3()
271
272    return
273
274
275if __name__=="__main__": 
276    main(["LeBailFitScript"])