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Wed Sep 7 04:38:51 2016 UTC (7 years, 6 months ago) by rtomiyasu
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The output format for base-centered monoclinic cells was corrected.
1 rtomiyasu 3 /*
2     * The MIT License
3    
4     Conograph (powder auto-indexing program)
5    
6     Copyright (c) <2012> <Ryoko Oishi-Tomiyasu, KEK>
7    
8     Permission is hereby granted, free of charge, to any person obtaining a copy
9     of this software and associated documentation files (the "Software"), to deal
10     in the Software without restriction, including without limitation the rights
11     to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
12     copies of the Software, and to permit persons to whom the Software is
13     furnished to do so, subject to the following conditions:
14    
15     The above copyright notice and this permission notice shall be included in
16     all copies or substantial portions of the Software.
17    
18     THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
19     IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
20     FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
21     AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
22     LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
23     OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
24     THE SOFTWARE.
25     *
26     */
27     #ifndef LatticeFigureOfMeritToDisplay_HH_
28     #define LatticeFigureOfMeritToDisplay_HH_
29    
30     #include <map>
31     #include "LatticeFigureOfMeritZeroShift.hh"
32     #include "../utility_data_structure/range.hh"
33 rtomiyasu 33 #include "../qc/reflection_conditions.hh"
34 rtomiyasu 3
35    
36     // Class for outputting information about a lattice in IGOR file.
37     class LatticeFigureOfMeritToDisplay
38     {
39     private:
40     LatticeFigureOfMeritZeroShift m_latfom;
41    
42     vector<QData> m_qdata;
43     vector< multimap<Double, vector<HKL_Q>::const_iterator> > m_associated_hkl_tray;
44     vector<HKL_Q> m_cal_hkl_tray;
45    
46     // The size of the following arrays equals zero or m_figures_of_merit.m_num_ref_figure_of_merit.
47     vector< VecDat3<Int4> > m_hkl_to_fit;
48     vector<bool> m_fix_or_fit_flag; // 0:fix, 1:fit.
49    
50 rtomiyasu 33 // If this is negative value, only the reflection conditions derived from the Bravais type are considered.
51     Int4 m_type_of_reflection_conditions;
52    
53 rtomiyasu 16 // for GUI
54     bool m_showsTicks;
55    
56     public:
57 rtomiyasu 3 void putPeakPosToFit(const ControlParam& cdata, Vec_DP& cal_q_tray, Vec_DP& cal_pos_tray) const;
58     void putStandardMillerIndicesToFit(vector< VecDat3<Int4> >& hkl_to_fit,
59     vector<bool>& fix_or_fit_flag) const;
60    
61     LatticeFigureOfMeritToDisplay();
62     ~LatticeFigureOfMeritToDisplay(){};
63    
64 rtomiyasu 25 inline const eBravaisType& enumBravaisType() const { return m_latfom.enumBravaisType(); };
65 rtomiyasu 3 inline const LatticeFigureOfMeritZeroShift& putLatticeFigureOfMerit() const { return m_latfom; };
66     inline const vector<HKL_Q>& putCalMillerIndices() const { return m_cal_hkl_tray; };
67     inline const vector< multimap<Double, vector<HKL_Q>::const_iterator> >& putAssociatedMillerIndices() const { return m_associated_hkl_tray; };
68    
69     // axis1: axis of the argument lattice constants for Monoclinic(C) or Orthorhombic(C).
70     // axis2: axis of the argument lattice constants for Rhombohedral.
71 rtomiyasu 25 inline ZErrorMessage setLatticeConstantsDegree(const eBravaisType& ecys,
72 rtomiyasu 3 const eABCaxis& axis1,
73     const eRHaxis& axis2,
74     const VecDat3<Double>& length_axis,
75     const VecDat3<Double>& angle_axis) { return m_latfom.setLatticeConstantsDegree(BravaisType(ecys, axis1, axis2), length_axis, angle_axis); };
76     inline ZErrorMessage setPeakShiftParamDegree(const ePeakShiftFunctionType& type,
77     const Double& wave_length,
78     const vector<ZParawError>& peak_shift_param_deg, // The errors are not used in this method.
79     const PeakPosData& pdata);
80     inline void reduceLatticeConstants();
81    
82     inline void putOptimizedLatticeConstantsDegree(const eABCaxis& axis1,
83     const eRHaxis& axis2,
84     VecDat3<Double>& length_axis,
85     VecDat3<Double>& angle_axis) { m_latfom.putOptimizedLatticeConstantsDegree(axis1, axis2, length_axis, angle_axis); };
86    
87     // axis1: axis of the argument lattice constants for Monoclinic(C) or Orthorhombic(C).
88     // axis2: axis of the argument lattice constants for Rhombohedral.
89     inline void putReducedLatticeConstantsDegree(const eABCaxis& axis1,
90     const eRHaxis& axis2,
91     VecDat3<Double>& length_axis,
92     VecDat3<Double>& angle_axis) { m_latfom.putReducedLatticeConstantsDegree(axis1, axis2, length_axis, angle_axis); };
93    
94 rtomiyasu 25 inline const Double& putWaveLength() const { return m_latfom.putWaveLength(); };
95 rtomiyasu 3 inline const ePeakShiftFunctionType& putPeakShiftFunctionType() const { return m_latfom.putPeakShiftFunctionType(); };
96     inline vector<ZParawError> putPeakShiftParamDegree() const { return m_latfom.putPeakShiftParamDegree(); };
97    
98     inline const vector<QData>& putQDataModifiedWithNewPeakShiftParam() const { return m_qdata; };
99    
100 rtomiyasu 33 inline void setDeWolffFigureOfMerit(const Int4& num_ref_figure_of_merit){ m_latfom.setDeWolffFigureOfMerit(num_ref_figure_of_merit, m_type_of_reflection_conditions, m_qdata); };
101 rtomiyasu 3 inline void setFigureOfMerit(const Int4& num_ref_figure_of_merit){ m_latfom.setFigureOfMerit(num_ref_figure_of_merit, m_qdata); };
102    
103 rtomiyasu 33 void setTypeOfSystematicAbsences(const Int4& arg);
104     inline string putShortStringTypeOfSystematicAbsences() const
105     {
106     return putInformationOnReflectionConditions(this->putLatticeFigureOfMerit().putBravaisType(), m_type_of_reflection_conditions).putShortStringType();
107     };
108     inline const string& putStringTypeOfSystematicAbsences() const
109     {
110     return putInformationOnReflectionConditions(this->putLatticeFigureOfMerit().putBravaisType(), m_type_of_reflection_conditions).putStringType();
111     };
112     inline const string& putStringReflectionConditions() const
113     {
114     return putInformationOnReflectionConditions(this->putLatticeFigureOfMerit().putBravaisType(), m_type_of_reflection_conditions).putStringConditions();
115     };
116     inline const DataReflectionConditions& putDataOnReflectionConditions() const
117     {
118     return putInformationOnReflectionConditions(this->putLatticeFigureOfMerit().putBravaisType(), m_type_of_reflection_conditions);
119     };
120    
121    
122 rtomiyasu 25 // Resets m_associated_hkl_tray and q-values in m_cal_hkl_tray.
123     void resetQValuesInRange(const Int4& num_fit_data);
124 rtomiyasu 3 // Resets m_associated_hkl_tray and m_cal_hkl_tray.
125     void resetMillerIndicesInRange(const Int4& num_fit_data);
126     // Resets m_hkl_to_fit and m_fix_or_fit_flag.
127     void resetMillerIndicesToFit() { putStandardMillerIndicesToFit(m_hkl_to_fit, m_fix_or_fit_flag); };
128    
129     inline ZErrorMessage setFittingIDs(const vector<bool>& arg);
130     inline const vector<bool>& putFittingIDs() const { return m_fix_or_fit_flag; };
131     inline ZErrorMessage setMillerIndicesToFit(const vector< VecDat3<Int4> >& arg);
132     inline const vector< VecDat3<Int4> >& putMillerIndicesToFit() const { return m_hkl_to_fit; };
133    
134     // Return peak positions for this lattice candidate.
135     void putCalculatedPeakPosInRange(const ControlParam& cdata, Vec_DP& cal_pos_tray) const;
136    
137     // Returned value
138     // > 1 : Optimization has succeeded at least twice. (The members m_hkl_to_fit and m_fix_or_fit_flag are changed.)
139     // > 0 : Optimization has succeeded. (Lattice constants are changed.)
140     // 0 : Optimization has failed.
141     Int4 fitLatticeParameter(const PeakPosData& pdata, const vector<etype_ID>& fitflag,
142     const Int4& Max_ITNUM,
143     const Double& limiter);
144    
145     // Output indexing results.
146     void printIndexingResult(const ControlParam& cdata,
147     const PeakPosData& pdata,
148     const Int4& label_start0,
149     ostream* os) const;
150    
151     // For GUI.
152     const vector<bool> &getref_m_fix_or_fit_flag() const {return m_fix_or_fit_flag;}
153     vector<bool> &getref_m_fix_or_fit_flag() {return m_fix_or_fit_flag;}
154     const vector<VecDat3<Int4> > &getref_m_hkl_to_fit() const {return m_hkl_to_fit;}
155     vector<VecDat3<Int4> > &getref_m_hkl_to_fit() {return m_hkl_to_fit;}
156 rtomiyasu 16 const LatticeFigureOfMeritZeroShift &getref_m_latfom() const {return m_latfom;}
157     LatticeFigureOfMeritZeroShift &getref_m_latfom() {return m_latfom;}
158     const vector<QData> &getref_m_qdata() const {return m_qdata;}
159     vector<QData> &getref_m_qdata() {return m_qdata;}
160     const vector< multimap<Double, vector<HKL_Q>::const_iterator> > &getref_m_associated_hkl_tray() const {return m_associated_hkl_tray;}
161     vector< multimap<Double, vector<HKL_Q>::const_iterator> > &getref_m_associated_hkl_tray() {return m_associated_hkl_tray;}
162     const vector<HKL_Q> &getref_m_cal_hkl_tray() const {return m_cal_hkl_tray;}
163     vector<HKL_Q> &getref_m_cal_hkl_tray() {return m_cal_hkl_tray;}
164     const bool &getref_m_showsTicks() const {return m_showsTicks;}
165     bool &getref_m_showsTicks() {return m_showsTicks;}
166 rtomiyasu 3 };
167    
168    
169     inline ZErrorMessage LatticeFigureOfMeritToDisplay::setFittingIDs(const vector<bool>& arg)
170     {
171     if( arg.size() != m_associated_hkl_tray.size() )
172     {
173     return ZErrorMessage(ZErrorArgmentSize, __FILE__, __LINE__, __FUNCTION__);
174     }
175     m_fix_or_fit_flag = arg;
176     return ZErrorMessage();
177     }
178    
179     inline ZErrorMessage LatticeFigureOfMeritToDisplay::setMillerIndicesToFit(const vector< VecDat3<Int4> >& arg)
180     {
181     if( arg.size() != m_associated_hkl_tray.size() )
182     {
183     return ZErrorMessage(ZErrorArgmentSize, __FILE__, __LINE__, __FUNCTION__);
184     }
185     m_hkl_to_fit = arg;
186     return ZErrorMessage();
187     };
188    
189    
190     inline ZErrorMessage LatticeFigureOfMeritToDisplay::setPeakShiftParamDegree(
191     const ePeakShiftFunctionType& type,
192     const Double& wave_length,
193     const vector<ZParawError>& peak_shift_param_deg,
194     const PeakPosData& pdata)
195     {
196     static const Double RadDeg = PI() / 180.0;
197    
198     vector<ZParawError> peak_shift_param_rad = peak_shift_param_deg;
199     for(vector<ZParawError>::iterator it=peak_shift_param_rad.begin(); it<peak_shift_param_rad.end(); it++)
200     {
201     *it *= RadDeg;
202     }
203     return m_latfom.setPeakShiftParamRadian(VCData::putPeakQData(), type, wave_length, peak_shift_param_rad, pdata,
204     VCData::putPeakQData().size(), m_qdata);
205     };
206    
207 rtomiyasu 33
208     inline VecDat3<Int4> product_hkl(const VecDat3<Int4>& lhs, const NRMat<Int4>& rhs)
209     {
210     assert( rhs.nrows() >= 3 && rhs.ncols() == 3 );
211    
212     VecDat3<Int4> ans;
213     ans[0] = lhs[0]*rhs[0][0] + lhs[1]*rhs[1][0] + lhs[2]*rhs[2][0];
214     ans[1] = lhs[0]*rhs[0][1] + lhs[1]*rhs[1][1] + lhs[2]*rhs[2][1];
215     ans[2] = lhs[0]*rhs[0][2] + lhs[1]*rhs[1][2] + lhs[2]*rhs[2][2];
216     return ans;
217     }
218    
219    
220 rtomiyasu 3 inline void LatticeFigureOfMeritToDisplay::reduceLatticeConstants()
221     {
222     NRMat<Int4> trans_mat;
223 rtomiyasu 33 // trans_mat * m_latfom.m_S_optimized.first(new) * transpose(trans_mat) = m_latfom.m_S_optimized.first(old).
224 rtomiyasu 3 m_latfom.reduceLatticeConstants(trans_mat);
225    
226     for(vector<HKL_Q>::iterator it=m_cal_hkl_tray.begin(); it<m_cal_hkl_tray.end(); it++)
227     {
228 rtomiyasu 25 it->setHKL( product_hkl(it->HKL(), trans_mat) );
229 rtomiyasu 3 }
230    
231     for(vector< VecDat3<Int4> >::iterator it=m_hkl_to_fit.begin(); it<m_hkl_to_fit.end(); it++)
232     {
233     *it = product_hkl(*it, trans_mat);
234     }
235     };
236    
237 rtomiyasu 33 inline bool cmpDeWolff(const LatticeFigureOfMeritToDisplay& lhs, const LatticeFigureOfMeritToDisplay& rhs)
238     {
239     return lhs.putLatticeFigureOfMerit().putFiguresOfMerit().putFigureOfMeritWolff()
240     > rhs.putLatticeFigureOfMerit().putFiguresOfMerit().putFigureOfMeritWolff();
241     }
242    
243    
244 rtomiyasu 3 #endif /*LatticeFigureOfMeritToDisplay_HH_*/
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