queso-0.53.0
SequenceStatisticalOptions.C
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1 //-----------------------------------------------------------------------bl-
2 //--------------------------------------------------------------------------
3 //
4 // QUESO - a library to support the Quantification of Uncertainty
5 // for Estimation, Simulation and Optimization
6 //
7 // Copyright (C) 2008-2015 The PECOS Development Team
8 //
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the Version 2.1 GNU Lesser General
11 // Public License as published by the Free Software Foundation.
12 //
13 // This library is distributed in the hope that it will be useful,
14 // but WITHOUT ANY WARRANTY; without even the implied warranty of
15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
16 // Lesser General Public License for more details.
17 //
18 // You should have received a copy of the GNU Lesser General Public
19 // License along with this library; if not, write to the Free Software
20 // Foundation, Inc. 51 Franklin Street, Fifth Floor,
21 // Boston, MA 02110-1301 USA
22 //
23 //-----------------------------------------------------------------------el-
24 
25 #include <queso/Defines.h>
26 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
27 
28 #include <boost/program_options.hpp>
29 
30 #include <queso/SequenceStatisticalOptions.h>
31 #include <queso/Miscellaneous.h>
32 
33 namespace QUESO {
34 
35 SsOptionsValues::SsOptionsValues()
36  :
37  m_prefix ("stats_"),
38  m_initialDiscardedPortions(0 ),//,0.),
39 #ifdef QUESO_COMPUTES_EXTRA_POST_PROCESSING_STATISTICS
40  m_meanMonitorPeriod (UQ_SEQUENCE_MEAN_MONITOR_PERIOD_ODV ),
41  m_bmmRun (UQ_SEQUENCE_BMM_RUN_ODV ),
42  m_bmmLengths (0 ),//,0),
43  m_fftCompute (UQ_SEQUENCE_FFT_COMPUTE_ODV ),
44  m_fftParamId (UQ_SEQUENCE_FFT_PARAM_ID_ODV ),
45  m_fftSize (UQ_SEQUENCE_FFT_SIZE_ODV ),
46  m_fftTestInversion (UQ_SEQUENCE_FFT_TEST_INVERSION_ODV ),
47  m_fftWrite (UQ_SEQUENCE_FFT_WRITE_ODV ),
48  m_psdCompute (UQ_SEQUENCE_PSD_COMPUTE_ODV ),
49  m_psdNumBlocks (UQ_SEQUENCE_PSD_NUM_BLOCKS_ODV ),
50  m_psdHopSizeRatio (UQ_SEQUENCE_PSD_HOP_SIZE_RATIO_ODV ),
51  m_psdParamId (UQ_SEQUENCE_PSD_PARAM_ID_ODV ),
52  m_psdWrite (UQ_SEQUENCE_PSD_WRITE_ODV ),
53  m_psdAtZeroCompute (UQ_SEQUENCE_PSD_AT_ZERO_COMPUTE_ODV ),
54  m_psdAtZeroNumBlocks (0 ),//,0),
55  m_psdAtZeroHopSizeRatio (UQ_SEQUENCE_PSD_AT_ZERO_HOP_SIZE_RATIO_ODV ),
56  m_psdAtZeroDisplay (UQ_SEQUENCE_PSD_AT_ZERO_DISPLAY_ODV ),
57  m_psdAtZeroWrite (UQ_SEQUENCE_PSD_AT_ZERO_WRITE_ODV ),
58  m_gewekeCompute (UQ_SEQUENCE_GEWEKE_COMPUTE_ODV ),
59  m_gewekeNaRatio (UQ_SEQUENCE_GEWEKE_NA_RATIO_ODV ),
60  m_gewekeNbRatio (UQ_SEQUENCE_GEWEKE_NB_RATIO_ODV ),
61  m_gewekeDisplay (UQ_SEQUENCE_GEWEKE_DISPLAY_ODV ),
62  m_gewekeWrite (UQ_SEQUENCE_GEWEKE_WRITE_ODV ),
63  m_meanStaccCompute (UQ_SEQUENCE_MEAN_STACC_COMPUTE_ODV ),
64  m_histCompute (UQ_SEQUENCE_HIST_COMPUTE_ODV ),
65  m_histNumInternalBins (UQ_SEQUENCE_HIST_NUM_INTERNAL_BINS_ODV ),
66  m_cdfStaccCompute (UQ_SEQUENCE_CDF_STACC_COMPUTE_ODV ),
67  m_cdfStaccNumEvalPositions(UQ_SEQUENCE_CDF_STACC_NUM_EVAL_POSITIONS_ODV),
68 #endif
69  m_autoCorrComputeViaDef (UQ_SEQUENCE_AUTO_CORR_COMPUTE_VIA_DEF_ODV ),
70  m_autoCorrComputeViaFft (UQ_SEQUENCE_AUTO_CORR_COMPUTE_VIA_FFT_ODV ),
71  m_autoCorrSecondLag (UQ_SEQUENCE_AUTO_CORR_SECOND_LAG_ODV ),
72  m_autoCorrLagSpacing (UQ_SEQUENCE_AUTO_CORR_LAG_SPACING_ODV ),
73  m_autoCorrNumLags (UQ_SEQUENCE_AUTO_CORR_NUM_LAGS_ODV ),
74  m_autoCorrDisplay (UQ_SEQUENCE_AUTO_CORR_DISPLAY_ODV ),
75  m_autoCorrWrite (UQ_SEQUENCE_AUTO_CORR_WRITE_ODV ),
76  m_kdeCompute (UQ_SEQUENCE_KDE_COMPUTE_ODV ),
77  m_kdeNumEvalPositions (UQ_SEQUENCE_KDE_NUM_EVAL_POSITIONS_ODV ),
78  m_covMatrixCompute (UQ_SEQUENCE_COV_MATRIX_COMPUTE_ODV ),
79  m_corrMatrixCompute (UQ_SEQUENCE_CORR_MATRIX_COMPUTE_ODV ),
80  m_option_help (m_prefix + "help" ),
81  m_option_initialDiscardedPortions (m_prefix + "initialDiscardedPortions" ),
82 #ifdef QUESO_COMPUTES_EXTRA_POST_PROCESSING_STATISTICS
83  m_option_mean_monitorPeriod (m_prefix + "mean_monitorPeriod" ),
84  m_option_bmm_run (m_prefix + "bmm_run" ),
85  m_option_bmm_lengths (m_prefix + "bmm_lengths" ),
86  m_option_bmm_display (m_prefix + "bmm_display" ),
87  m_option_bmm_write (m_prefix + "bmm_write" ),
88  m_option_fft_compute (m_prefix + "fft_compute" ),
89  m_option_fft_paramId (m_prefix + "fft_paramId" ),
90  m_option_fft_size (m_prefix + "fft_size" ),
91  m_option_fft_testInversion (m_prefix + "fft_testInversion" ),
92  m_option_fft_write (m_prefix + "fft_write" ),
93  m_option_psd_compute (m_prefix + "psd_compute" ),
94  m_option_psd_numBlocks (m_prefix + "psd_numBlocks" ),
95  m_option_psd_hopSizeRatio (m_prefix + "psd_hopSizeRatio" ),
96  m_option_psd_paramId (m_prefix + "psd_paramId" ),
97  m_option_psd_write (m_prefix + "psd_write" ),
98  m_option_psdAtZero_compute (m_prefix + "psdAtZero_compute" ),
99  m_option_psdAtZero_numBlocks (m_prefix + "psdAtZero_numBlocks" ),
100  m_option_psdAtZero_hopSizeRatio (m_prefix + "psdAtZero_hopSizeRatio" ),
101  m_option_psdAtZero_display (m_prefix + "psdAtZero_display" ),
102  m_option_psdAtZero_write (m_prefix + "psdAtZero_write" ),
103  m_option_geweke_compute (m_prefix + "geweke_compute" ),
104  m_option_geweke_naRatio (m_prefix + "geweke_naRatio" ),
105  m_option_geweke_nbRatio (m_prefix + "geweke_nbRatio" ),
106  m_option_geweke_display (m_prefix + "geweke_display" ),
107  m_option_geweke_write (m_prefix + "geweke_write" ),
108  m_option_meanStacc_compute (m_prefix + "meanStacc_compute" ),
109  m_option_hist_compute (m_prefix + "hist_compute" ),
110  m_option_hist_numInternalBins (m_prefix + "hist_numInternalBins" ),
111  m_option_cdfStacc_compute (m_prefix + "cdfStacc_compute" ),
112  m_option_cdfStacc_numEvalPositions(m_prefix + "cdfStacc_numEvalPositions"),
113 #endif
114  m_option_autoCorr_computeViaDef (m_prefix + "autoCorr_computeViaDef" ),
115  m_option_autoCorr_computeViaFft (m_prefix + "autoCorr_computeViaFft" ),
116  m_option_autoCorr_secondLag (m_prefix + "autoCorr_secondLag" ),
117  m_option_autoCorr_lagSpacing (m_prefix + "autoCorr_lagSpacing" ),
118  m_option_autoCorr_numLags (m_prefix + "autoCorr_numLags" ),
119  m_option_autoCorr_display (m_prefix + "autoCorr_display" ),
120  m_option_autoCorr_write (m_prefix + "autoCorr_write" ),
121  m_option_kde_compute (m_prefix + "kde_compute" ),
122  m_option_kde_numEvalPositions (m_prefix + "kde_numEvalPositions" ),
123  m_option_covMatrix_compute (m_prefix + "covMatrix_compute" ),
124  m_option_corrMatrix_compute (m_prefix + "corrMatrix_compute" )
125 {
126 }
127 
128 SsOptionsValues::SsOptionsValues(const BaseEnvironment * env, const char *
129  prefix)
130  :
131  m_prefix ((std::string)(prefix) + "stats_"),
132  m_initialDiscardedPortions(0 ),//,0.),
133 #ifdef QUESO_COMPUTES_EXTRA_POST_PROCESSING_STATISTICS
134  m_meanMonitorPeriod (UQ_SEQUENCE_MEAN_MONITOR_PERIOD_ODV ),
135  m_bmmRun (UQ_SEQUENCE_BMM_RUN_ODV ),
136  m_bmmLengths (0 ),//,0),
137  m_fftCompute (UQ_SEQUENCE_FFT_COMPUTE_ODV ),
138  m_fftParamId (UQ_SEQUENCE_FFT_PARAM_ID_ODV ),
139  m_fftSize (UQ_SEQUENCE_FFT_SIZE_ODV ),
140  m_fftTestInversion (UQ_SEQUENCE_FFT_TEST_INVERSION_ODV ),
141  m_fftWrite (UQ_SEQUENCE_FFT_WRITE_ODV ),
142  m_psdCompute (UQ_SEQUENCE_PSD_COMPUTE_ODV ),
143  m_psdNumBlocks (UQ_SEQUENCE_PSD_NUM_BLOCKS_ODV ),
144  m_psdHopSizeRatio (UQ_SEQUENCE_PSD_HOP_SIZE_RATIO_ODV ),
145  m_psdParamId (UQ_SEQUENCE_PSD_PARAM_ID_ODV ),
146  m_psdWrite (UQ_SEQUENCE_PSD_WRITE_ODV ),
147  m_psdAtZeroCompute (UQ_SEQUENCE_PSD_AT_ZERO_COMPUTE_ODV ),
148  m_psdAtZeroNumBlocks (0 ),//,0),
149  m_psdAtZeroHopSizeRatio (UQ_SEQUENCE_PSD_AT_ZERO_HOP_SIZE_RATIO_ODV ),
150  m_psdAtZeroDisplay (UQ_SEQUENCE_PSD_AT_ZERO_DISPLAY_ODV ),
151  m_psdAtZeroWrite (UQ_SEQUENCE_PSD_AT_ZERO_WRITE_ODV ),
152  m_gewekeCompute (UQ_SEQUENCE_GEWEKE_COMPUTE_ODV ),
153  m_gewekeNaRatio (UQ_SEQUENCE_GEWEKE_NA_RATIO_ODV ),
154  m_gewekeNbRatio (UQ_SEQUENCE_GEWEKE_NB_RATIO_ODV ),
155  m_gewekeDisplay (UQ_SEQUENCE_GEWEKE_DISPLAY_ODV ),
156  m_gewekeWrite (UQ_SEQUENCE_GEWEKE_WRITE_ODV ),
157  m_meanStaccCompute (UQ_SEQUENCE_MEAN_STACC_COMPUTE_ODV ),
158  m_histCompute (UQ_SEQUENCE_HIST_COMPUTE_ODV ),
159  m_histNumInternalBins (UQ_SEQUENCE_HIST_NUM_INTERNAL_BINS_ODV ),
160  m_cdfStaccCompute (UQ_SEQUENCE_CDF_STACC_COMPUTE_ODV ),
161  m_cdfStaccNumEvalPositions(UQ_SEQUENCE_CDF_STACC_NUM_EVAL_POSITIONS_ODV),
162 #endif
163  m_autoCorrComputeViaDef (UQ_SEQUENCE_AUTO_CORR_COMPUTE_VIA_DEF_ODV ),
164  m_autoCorrComputeViaFft (UQ_SEQUENCE_AUTO_CORR_COMPUTE_VIA_FFT_ODV ),
165  m_autoCorrSecondLag (UQ_SEQUENCE_AUTO_CORR_SECOND_LAG_ODV ),
166  m_autoCorrLagSpacing (UQ_SEQUENCE_AUTO_CORR_LAG_SPACING_ODV ),
167  m_autoCorrNumLags (UQ_SEQUENCE_AUTO_CORR_NUM_LAGS_ODV ),
168  m_autoCorrDisplay (UQ_SEQUENCE_AUTO_CORR_DISPLAY_ODV ),
169  m_autoCorrWrite (UQ_SEQUENCE_AUTO_CORR_WRITE_ODV ),
170  m_kdeCompute (UQ_SEQUENCE_KDE_COMPUTE_ODV ),
171  m_kdeNumEvalPositions (UQ_SEQUENCE_KDE_NUM_EVAL_POSITIONS_ODV ),
172  m_covMatrixCompute (UQ_SEQUENCE_COV_MATRIX_COMPUTE_ODV ),
173  m_corrMatrixCompute (UQ_SEQUENCE_CORR_MATRIX_COMPUTE_ODV ),
174  m_parser(new BoostInputOptionsParser(env->optionsInputFileName())),
175  m_option_help (m_prefix + "help" ),
176  m_option_initialDiscardedPortions (m_prefix + "initialDiscardedPortions" ),
177 #ifdef QUESO_COMPUTES_EXTRA_POST_PROCESSING_STATISTICS
178  m_option_mean_monitorPeriod (m_prefix + "mean_monitorPeriod" ),
179  m_option_bmm_run (m_prefix + "bmm_run" ),
180  m_option_bmm_lengths (m_prefix + "bmm_lengths" ),
181  m_option_bmm_display (m_prefix + "bmm_display" ),
182  m_option_bmm_write (m_prefix + "bmm_write" ),
183  m_option_fft_compute (m_prefix + "fft_compute" ),
184  m_option_fft_paramId (m_prefix + "fft_paramId" ),
185  m_option_fft_size (m_prefix + "fft_size" ),
186  m_option_fft_testInversion (m_prefix + "fft_testInversion" ),
187  m_option_fft_write (m_prefix + "fft_write" ),
188  m_option_psd_compute (m_prefix + "psd_compute" ),
189  m_option_psd_numBlocks (m_prefix + "psd_numBlocks" ),
190  m_option_psd_hopSizeRatio (m_prefix + "psd_hopSizeRatio" ),
191  m_option_psd_paramId (m_prefix + "psd_paramId" ),
192  m_option_psd_write (m_prefix + "psd_write" ),
193  m_option_psdAtZero_compute (m_prefix + "psdAtZero_compute" ),
194  m_option_psdAtZero_numBlocks (m_prefix + "psdAtZero_numBlocks" ),
195  m_option_psdAtZero_hopSizeRatio (m_prefix + "psdAtZero_hopSizeRatio" ),
196  m_option_psdAtZero_display (m_prefix + "psdAtZero_display" ),
197  m_option_psdAtZero_write (m_prefix + "psdAtZero_write" ),
198  m_option_geweke_compute (m_prefix + "geweke_compute" ),
199  m_option_geweke_naRatio (m_prefix + "geweke_naRatio" ),
200  m_option_geweke_nbRatio (m_prefix + "geweke_nbRatio" ),
201  m_option_geweke_display (m_prefix + "geweke_display" ),
202  m_option_geweke_write (m_prefix + "geweke_write" ),
203  m_option_meanStacc_compute (m_prefix + "meanStacc_compute" ),
204  m_option_hist_compute (m_prefix + "hist_compute" ),
205  m_option_hist_numInternalBins (m_prefix + "hist_numInternalBins" ),
206  m_option_cdfStacc_compute (m_prefix + "cdfStacc_compute" ),
207  m_option_cdfStacc_numEvalPositions(m_prefix + "cdfStacc_numEvalPositions"),
208 #endif
209  m_option_autoCorr_computeViaDef (m_prefix + "autoCorr_computeViaDef" ),
210  m_option_autoCorr_computeViaFft (m_prefix + "autoCorr_computeViaFft" ),
211  m_option_autoCorr_secondLag (m_prefix + "autoCorr_secondLag" ),
212  m_option_autoCorr_lagSpacing (m_prefix + "autoCorr_lagSpacing" ),
213  m_option_autoCorr_numLags (m_prefix + "autoCorr_numLags" ),
214  m_option_autoCorr_display (m_prefix + "autoCorr_display" ),
215  m_option_autoCorr_write (m_prefix + "autoCorr_write" ),
216  m_option_kde_compute (m_prefix + "kde_compute" ),
217  m_option_kde_numEvalPositions (m_prefix + "kde_numEvalPositions" ),
218  m_option_covMatrix_compute (m_prefix + "covMatrix_compute" ),
219  m_option_corrMatrix_compute (m_prefix + "corrMatrix_compute" )
220 {
221  (m_option_help, "produce help message for chain statistical options" )
222  (m_option_initialDiscardedPortions, boost::program_options::value<std::string >()->default_value(UQ_SEQUENCE_INITIAL_DISCARDED_PORTIONS_ODV ), "list of initial discarded portions for chain statistics" )
223 #ifdef QUESO_COMPUTES_EXTRA_POST_PROCESSING_STATISTICS
224  m_parser->registerOption(m_option_mean_monitorPeriod, UQ_SEQUENCE_MEAN_MONITOR_PERIOD_ODV, "period for monitoring mean" );
225  m_parser->registerOption(m_option_bmm_run, UQ_SEQUENCE_BMM_RUN_ODV , "compute variance of sample mean with batch means method" );
226  m_parser->registerOption<std::string>(m_option_bmm_lengths, UQ_SEQUENCE_BMM_LENGTHS_ODV , "list of batch lenghts for BMM" );
227  m_parser->registerOption(m_option_fft_compute, UQ_SEQUENCE_FFT_COMPUTE_ODV , "compute fft" );
228  m_parser->registerOption(m_option_fft_paramId, UQ_SEQUENCE_FFT_PARAM_ID_ODV , "parameter id for fft computations" );
229  m_parser->registerOption(m_option_fft_size, UQ_SEQUENCE_FFT_SIZE_ODV , "fft size" );
230  m_parser->registerOption(m_option_fft_testInversion, UQ_SEQUENCE_FFT_TEST_INVERSION_ODV , "test fft inversion" );
231  m_parser->registerOption(m_option_fft_write, UQ_SEQUENCE_FFT_WRITE_ODV , "write fft" );
232  m_parser->registerOption(m_option_psd_compute, UQ_SEQUENCE_PSD_COMPUTE_ODV , "compute psd" );
233  m_parser->registerOption(m_option_psd_numBlocks, UQ_SEQUENCE_PSD_NUM_BLOCKS_ODV , "number of blocks for computation of psd" );
234  m_parser->registerOption(m_option_psd_hopSizeRatio, UQ_SEQUENCE_PSD_HOP_SIZE_RATIO_ODV , "hop size ratio for psd" );
235  m_parser->registerOption(m_option_psd_paramId, UQ_SEQUENCE_PSD_PARAM_ID_ODV , "parameter id for psd computations" );
236  m_parser->registerOption(m_option_psd_write, UQ_SEQUENCE_PSD_WRITE_ODV , "write psd" );
237  m_parser->registerOption(m_option_psdAtZero_compute, UQ_SEQUENCE_PSD_AT_ZERO_COMPUTE_ODV, "compute power spectral densities" );
238  m_parser->registerOption<std::string>(m_option_psdAtZero_numBlocks, UQ_SEQUENCE_PSD_AT_ZERO_NUM_BLOCKS_ODV , "list of numbers of blocks for computation of psd at zero" );
239  m_parser->registerOption(m_option_psdAtZero_hopSizeRatio, UQ_SEQUENCE_PSD_AT_ZERO_HOP_SIZE_RATIO_ODV , "hop size ratio for psd at zero" );
240  m_parser->registerOption(m_option_psdAtZero_display, UQ_SEQUENCE_PSD_AT_ZERO_DISPLAY_ODV, "display computed psd at frequency zero on screen" );
241  m_parser->registerOption(m_option_psdAtZero_write, UQ_SEQUENCE_PSD_AT_ZERO_WRITE_ODV , "write computed psd at frequency zero to the output file" );
242  m_parser->registerOption(m_option_geweke_compute, UQ_SEQUENCE_GEWEKE_COMPUTE_ODV , "compute Geweke coefficients" );
243  m_parser->registerOption(m_option_geweke_naRatio, UQ_SEQUENCE_GEWEKE_NA_RATIO_ODV , "ratio NA for Geweke" );
244  m_parser->registerOption(m_option_geweke_nbRatio, UQ_SEQUENCE_GEWEKE_NB_RATIO_ODV , "ratio NB for Geweke" );
245  m_parser->registerOption(m_option_geweke_display, UQ_SEQUENCE_GEWEKE_DISPLAY_ODV , "display computed Geweke on screen" );
246  m_parser->registerOption(m_option_geweke_write, UQ_SEQUENCE_GEWEKE_WRITE_ODV , "write computed Geweke to the output file" );
247  m_parser->registerOption(m_option_meanStacc_compute, UQ_SEQUENCE_MEAN_STACC_COMPUTE_ODV , "compute statistical accuracy of mean" );
248  m_parser->registerOption(m_option_hist_compute, UQ_SEQUENCE_HIST_COMPUTE_ODV , "compute histograms" );
249  m_parser->registerOption(m_option_hist_numInternalBins, UQ_SEQUENCE_HIST_NUM_INTERNAL_BINS_ODV , "number of internal bins" );
250  m_parser->registerOption(m_option_cdfStacc_compute, UQ_SEQUENCE_CDF_STACC_COMPUTE_ODV , "compute statisical accuracy of cdf" );
251  m_parser->registerOption(m_option_cdfStacc_numEvalPositions, UQ_SEQUENCE_CDF_STACC_NUM_EVAL_POSITIONS_ODV , "number of evaluations points for statistical accuracy of cdf" );
252 #endif
253  m_parser->registerOption(m_option_autoCorr_computeViaDef, boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_AUTO_CORR_COMPUTE_VIA_DEF_ODV ), "compute correlations via definition" )
254  m_parser->registerOption(m_option_autoCorr_computeViaFft, boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_AUTO_CORR_COMPUTE_VIA_FFT_ODV ), "compute correlations via fft" )
255  m_parser->registerOption(m_option_autoCorr_secondLag, boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_AUTO_CORR_SECOND_LAG_ODV ), "second lag for computation of autocorrelations" )
256  m_parser->registerOption(m_option_autoCorr_lagSpacing, boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_AUTO_CORR_LAG_SPACING_ODV ), "lag spacing for computation of autocorrelations" )
257  m_parser->registerOption(m_option_autoCorr_numLags, boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_AUTO_CORR_NUM_LAGS_ODV ), "number of lags for computation of autocorrelations" )
258  m_parser->registerOption(m_option_autoCorr_display, boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_AUTO_CORR_DISPLAY_ODV ), "display computed autocorrelations on the screen" )
259  m_parser->registerOption(m_option_autoCorr_write, boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_AUTO_CORR_WRITE_ODV ), "write computed autocorrelations to the output file" )
260  m_parser->registerOption(m_option_kde_compute, boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_KDE_COMPUTE_ODV ), "compute kernel density estimators" )
261  m_parser->registerOption(m_option_kde_numEvalPositions, boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_KDE_NUM_EVAL_POSITIONS_ODV ), "number of evaluation positions" )
262  m_parser->registerOption(m_option_covMatrix_compute, boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_COV_MATRIX_COMPUTE_ODV ), "compute covariance matrix" )
263  m_parser->registerOption(m_option_corrMatrix_compute, boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_CORR_MATRIX_COMPUTE_ODV ), "compute correlation matrix" )
264 }
265 
266 SsOptionsValues::~SsOptionsValues()
267 {
268 }
269 
270 SsOptionsValues::SsOptionsValues(const SsOptionsValues& src)
271 {
272  this->copy(src);
273 }
274 
275 SsOptionsValues&
276 SsOptionsValues::operator=(const SsOptionsValues& rhs)
277 {
278  this->copy(rhs);
279  return *this;
280 }
281 
282 void
283 SsOptionsValues::defineOptions()
284 {
285  (*m_optionsDescription).add_options()
286  (m_option_help.c_str(), "produce help message for chain statistical options" )
287  (m_option_initialDiscardedPortions.c_str(), boost::program_options::value<std::string >()->default_value(UQ_SEQUENCE_INITIAL_DISCARDED_PORTIONS_ODV ), "list of initial discarded portions for chain statistics" )
288 #ifdef QUESO_COMPUTES_EXTRA_POST_PROCESSING_STATISTICS
289  (m_option_mean_monitorPeriod.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_MEAN_MONITOR_PERIOD_ODV ), "period for monitoring mean" )
290  (m_option_bmm_run.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_BMM_RUN_ODV ), "compute variance of sample mean with batch means method" )
291  (m_option_bmm_lengths.c_str(), boost::program_options::value<std::string >()->default_value(UQ_SEQUENCE_BMM_LENGTHS_ODV ), "list of batch lenghts for BMM" )
292  (m_option_fft_compute.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_FFT_COMPUTE_ODV ), "compute fft" )
293  (m_option_fft_paramId.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_FFT_PARAM_ID_ODV ), "parameter id for fft computations" )
294  (m_option_fft_size.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_FFT_SIZE_ODV ), "fft size" )
295  (m_option_fft_testInversion.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_FFT_TEST_INVERSION_ODV ), "test fft inversion" )
296  (m_option_fft_write.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_FFT_WRITE_ODV ), "write fft" )
297  (m_option_psd_compute.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_PSD_COMPUTE_ODV ), "compute psd" )
298  (m_option_psd_numBlocks.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_PSD_NUM_BLOCKS_ODV ), "number of blocks for computation of psd" )
299  (m_option_psd_hopSizeRatio.c_str(), boost::program_options::value<double >()->default_value(UQ_SEQUENCE_PSD_HOP_SIZE_RATIO_ODV ), "hop size ratio for psd" )
300  (m_option_psd_paramId.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_PSD_PARAM_ID_ODV ), "parameter id for psd computations" )
301  (m_option_psd_write.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_PSD_WRITE_ODV ), "write psd" )
302  (m_option_psdAtZero_compute.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_PSD_AT_ZERO_COMPUTE_ODV ), "compute power spectral densities" )
303  (m_option_psdAtZero_numBlocks.c_str(), boost::program_options::value<std::string >()->default_value(UQ_SEQUENCE_PSD_AT_ZERO_NUM_BLOCKS_ODV ), "list of numbers of blocks for computation of psd at zero" )
304  (m_option_psdAtZero_hopSizeRatio.c_str(), boost::program_options::value<double >()->default_value(UQ_SEQUENCE_PSD_AT_ZERO_HOP_SIZE_RATIO_ODV ), "hop size ratio for psd at zero" )
305  (m_option_psdAtZero_display.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_PSD_AT_ZERO_DISPLAY_ODV ), "display computed psd at frequency zero on screen" )
306  (m_option_psdAtZero_write.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_PSD_AT_ZERO_WRITE_ODV ), "write computed psd at frequency zero to the output file" )
307  (m_option_geweke_compute.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_GEWEKE_COMPUTE_ODV ), "compute Geweke coefficients" )
308  (m_option_geweke_naRatio.c_str(), boost::program_options::value<double >()->default_value(UQ_SEQUENCE_GEWEKE_NA_RATIO_ODV ), "ratio NA for Geweke" )
309  (m_option_geweke_nbRatio.c_str(), boost::program_options::value<double >()->default_value(UQ_SEQUENCE_GEWEKE_NB_RATIO_ODV ), "ratio NB for Geweke" )
310  (m_option_geweke_display.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_GEWEKE_DISPLAY_ODV ), "display computed Geweke on screen" )
311  (m_option_geweke_write.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_GEWEKE_WRITE_ODV ), "write computed Geweke to the output file" )
312  (m_option_meanStacc_compute.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_MEAN_STACC_COMPUTE_ODV ), "compute statistical accuracy of mean" )
313  (m_option_hist_compute.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_HIST_COMPUTE_ODV ), "compute histograms" )
314  (m_option_hist_numInternalBins.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_HIST_NUM_INTERNAL_BINS_ODV ), "number of internal bins" )
315  (m_option_cdfStacc_compute.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_CDF_STACC_COMPUTE_ODV ), "compute statisical accuracy of cdf" )
316  (m_option_cdfStacc_numEvalPositions.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_CDF_STACC_NUM_EVAL_POSITIONS_ODV ), "number of evaluations points for statistical accuracy of cdf" )
317 #endif
318  (m_option_autoCorr_computeViaDef.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_AUTO_CORR_COMPUTE_VIA_DEF_ODV ), "compute correlations via definition" )
319  (m_option_autoCorr_computeViaFft.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_AUTO_CORR_COMPUTE_VIA_FFT_ODV ), "compute correlations via fft" )
320  (m_option_autoCorr_secondLag.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_AUTO_CORR_SECOND_LAG_ODV ), "second lag for computation of autocorrelations" )
321  (m_option_autoCorr_lagSpacing.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_AUTO_CORR_LAG_SPACING_ODV ), "lag spacing for computation of autocorrelations" )
322  (m_option_autoCorr_numLags.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_AUTO_CORR_NUM_LAGS_ODV ), "number of lags for computation of autocorrelations" )
323  (m_option_autoCorr_display.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_AUTO_CORR_DISPLAY_ODV ), "display computed autocorrelations on the screen" )
324  (m_option_autoCorr_write.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_AUTO_CORR_WRITE_ODV ), "write computed autocorrelations to the output file" )
325  (m_option_kde_compute.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_KDE_COMPUTE_ODV ), "compute kernel density estimators" )
326  (m_option_kde_numEvalPositions.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_KDE_NUM_EVAL_POSITIONS_ODV ), "number of evaluation positions" )
327  (m_option_covMatrix_compute.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_COV_MATRIX_COMPUTE_ODV ), "compute covariance matrix" )
328  (m_option_corrMatrix_compute.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_CORR_MATRIX_COMPUTE_ODV ), "compute correlation matrix" )
329  ;
330 }
331 
332 void
333 SsOptionsValues::getOptionValues()
334 {
335  if ((*m_optionsMap).count(m_option_help)) {
336  if (m_env->subDisplayFile()) {
337  *m_env->subDisplayFile() << (*m_optionsDescription)
338  << std::endl;
339  }
340  }
341 
342  if ((*m_optionsMap).count(m_option_initialDiscardedPortions)) {
343  m_initialDiscardedPortions.clear();
344  std::vector<double> tmpPortions(0,0.);
345  std::string inputString = (*m_optionsMap)[m_option_initialDiscardedPortions].as<std::string>();
346  MiscReadDoublesFromString(inputString,tmpPortions);
347  //if (m_env->subDisplayFile()) {
348  // *m_env->subDisplayFile() << "In SequenceStatisticalOptions::getMyOptionValues(): percents = ";
349  // for (unsigned int i = 0; i < tmpPortions.size(); ++i) {
350  // *m_env->subDisplayFile() << " " << tmpPortions[i];
351  // }
352  // *m_env->subDisplayFile() << std::endl;
353  //}
354 
355  if (tmpPortions.size() > 0) {
356  m_initialDiscardedPortions.resize(tmpPortions.size(),0.);
357  for (unsigned int i = 0; i < m_initialDiscardedPortions.size(); ++i) {
358  m_initialDiscardedPortions[i] = tmpPortions[i];
359  }
360  }
361  }
362 
363 #ifdef QUESO_COMPUTES_EXTRA_POST_PROCESSING_STATISTICS
364  if ((*m_optionsMap).count(m_option_mean_monitorPeriod)) {
365  m_meanMonitorPeriod = (*m_optionsMap)[m_option_mean_monitorPeriod].as<unsigned int>();
366  }
367 
368  if ((*m_optionsMap).count(m_option_bmm_run)) {
369  m_bmmRun = (*m_optionsMap)[m_option_bmm_run].as<bool>();
370  }
371 
372  if ((*m_optionsMap).count(m_option_bmm_lengths)) {
373  m_bmmLengths.clear();
374  std::vector<double> tmpLengths(0,0.);
375  std::string inputString = (*m_optionsMap)[m_option_bmm_lengths].as<std::string>();
376  MiscReadDoublesFromString(inputString,tmpLengths);
377  //if (m_env->subDisplayFile()) {
378  // *m_env->subDisplayFile() << "In SequenceStatisticalOptions::getMyOptionValues(): lengths for BMM = ";
379  // for (unsigned int i = 0; i < tmpLengths.size(); ++i) {
380  // *m_env->subDisplayFile() << " " << tmpLengths[i];
381  // }
382  // *m_env->subDisplayFile() << std::endl;
383  //}
384 
385  if (tmpLengths.size() > 0) {
386  m_bmmLengths.resize(tmpLengths.size(),0);
387  for (unsigned int i = 0; i < m_bmmLengths.size(); ++i) {
388  m_bmmLengths[i] = (unsigned int) tmpLengths[i];
389  }
390  }
391  }
392 
393  if ((*m_optionsMap).count(m_option_fft_compute)) {
394  m_fftCompute = (*m_optionsMap)[m_option_fft_compute].as<bool>();
395  }
396 
397  if ((*m_optionsMap).count(m_option_fft_paramId)) {
398  m_fftParamId = (*m_optionsMap)[m_option_fft_paramId].as<unsigned int>();
399  }
400 
401  if ((*m_optionsMap).count(m_option_fft_size)) {
402  m_fftSize = (*m_optionsMap)[m_option_fft_size].as<unsigned int>();
403  }
404 
405  if ((*m_optionsMap).count(m_option_fft_testInversion)) {
406  m_fftTestInversion = (*m_optionsMap)[m_option_fft_testInversion].as<bool>();
407  }
408 
409  if ((*m_optionsMap).count(m_option_fft_write)) {
410  m_fftWrite = (*m_optionsMap)[m_option_fft_write].as<bool>();
411  }
412 
413  if ((*m_optionsMap).count(m_option_psd_compute)) {
414  m_psdCompute = (*m_optionsMap)[m_option_psd_compute].as<bool>();
415  }
416 
417  if ((*m_optionsMap).count(m_option_psd_numBlocks)) {
418  m_psdNumBlocks = (*m_optionsMap)[m_option_psd_numBlocks].as<unsigned int>();
419  }
420 
421  if ((*m_optionsMap).count(m_option_psd_hopSizeRatio)) {
422  m_psdHopSizeRatio = (*m_optionsMap)[m_option_psd_hopSizeRatio].as<double>();
423  }
424 
425  if ((*m_optionsMap).count(m_option_psd_paramId)) {
426  m_psdParamId = (*m_optionsMap)[m_option_psd_paramId].as<unsigned int>();
427  }
428 
429  if ((*m_optionsMap).count(m_option_psd_write)) {
430  m_psdWrite = (*m_optionsMap)[m_option_psd_write].as<bool>();
431  }
432 
433  if ((*m_optionsMap).count(m_option_psdAtZero_compute)) {
434  m_psdAtZeroCompute = (*m_optionsMap)[m_option_psdAtZero_compute].as<bool>();
435  }
436 
437  if ((*m_optionsMap).count(m_option_psdAtZero_numBlocks)) {
438  m_psdAtZeroNumBlocks.clear();
439  std::vector<double> tmpNumBlocks(0,0.);
440  std::string inputString = (*m_optionsMap)[m_option_psdAtZero_numBlocks].as<std::string>();
441  MiscReadDoublesFromString(inputString,tmpNumBlocks);
442  //if (m_env->subDisplayFile()) {
443  // *m_env->subDisplayFile() << "In SequenceStatisticalOptions::getMyOptionValues(): numBlocks for psdAtZero = ";
444  // for (unsigned int i = 0; i < tmpNumBlocks.size(); ++i) {
445  // *m_env->subDisplayFile() << " " << numBlocks[i];
446  // }
447  // *m_env->subDisplayFile() << std::endl;
448  //}
449 
450  if (tmpNumBlocks.size() > 0) {
451  m_psdAtZeroNumBlocks.resize(tmpNumBlocks.size(),0);
452  for (unsigned int i = 0; i < m_psdAtZeroNumBlocks.size(); ++i) {
453  m_psdAtZeroNumBlocks[i] = (unsigned int) tmpNumBlocks[i];
454  }
455  }
456  }
457 
458  if ((*m_optionsMap).count(m_option_psdAtZero_hopSizeRatio)) {
459  m_psdAtZeroHopSizeRatio = (*m_optionsMap)[m_option_psdAtZero_hopSizeRatio].as<double>();
460  }
461 
462  if ((*m_optionsMap).count(m_option_psdAtZero_display)) {
463  m_psdAtZeroDisplay = (*m_optionsMap)[m_option_psdAtZero_display].as<bool>();
464  }
465 
466  if ((*m_optionsMap).count(m_option_psdAtZero_write)) {
467  m_psdAtZeroWrite = (*m_optionsMap)[m_option_psdAtZero_write].as<bool>();
468  }
469 
470  if ((*m_optionsMap).count(m_option_geweke_compute)) {
471  m_gewekeCompute = (*m_optionsMap)[m_option_geweke_compute].as<bool>();
472  }
473 
474  if ((*m_optionsMap).count(m_option_geweke_naRatio)) {
475  m_gewekeNaRatio = (*m_optionsMap)[m_option_geweke_naRatio].as<double>();
476  }
477 
478  if ((*m_optionsMap).count(m_option_geweke_nbRatio)) {
479  m_gewekeNbRatio = (*m_optionsMap)[m_option_geweke_nbRatio].as<double>();
480  }
481 
482  if ((*m_optionsMap).count(m_option_geweke_display)) {
483  m_gewekeDisplay = (*m_optionsMap)[m_option_geweke_display].as<bool>();
484  }
485 
486  if ((*m_optionsMap).count(m_option_geweke_write)) {
487  m_gewekeWrite = (*m_optionsMap)[m_option_geweke_write].as<bool>();
488  }
489 
490  if ((*m_optionsMap).count(m_option_meanStacc_compute)) {
491  m_meanStaccCompute = (*m_optionsMap)[m_option_meanStacc_compute].as<bool>();
492  }
493 
494  if ((*m_optionsMap).count(m_option_hist_compute)) {
495  m_histCompute = (*m_optionsMap)[m_option_hist_compute].as<bool>();
496  }
497 
498  if ((*m_optionsMap).count(m_option_hist_numInternalBins)) {
499  m_histNumInternalBins = (*m_optionsMap)[m_option_hist_numInternalBins].as<unsigned int>();
500  }
501 
502  if ((*m_optionsMap).count(m_option_cdfStacc_compute)) {
503  m_cdfStaccCompute = (*m_optionsMap)[m_option_cdfStacc_compute].as<bool>();
504  }
505 
506  if ((*m_optionsMap).count(m_option_cdfStacc_numEvalPositions)) {
507  m_cdfStaccNumEvalPositions = (*m_optionsMap)[m_option_cdfStacc_numEvalPositions].as<unsigned int>();
508  }
509 #endif
510  if ((*m_optionsMap).count(m_option_autoCorr_computeViaDef)) {
511  m_autoCorrComputeViaDef = (*m_optionsMap)[m_option_autoCorr_computeViaDef].as<bool>();
512  }
513 
514  if ((*m_optionsMap).count(m_option_autoCorr_computeViaFft)) {
515  m_autoCorrComputeViaFft = (*m_optionsMap)[m_option_autoCorr_computeViaFft].as<bool>();
516  }
517 
518  if ((*m_optionsMap).count(m_option_autoCorr_secondLag)) {
519  m_autoCorrSecondLag = (*m_optionsMap)[m_option_autoCorr_secondLag].as<unsigned int>();
520  }
521 
522  if ((*m_optionsMap).count(m_option_autoCorr_lagSpacing)) {
523  m_autoCorrLagSpacing = (*m_optionsMap)[m_option_autoCorr_lagSpacing].as<unsigned int>();
524  }
525 
526  if ((*m_optionsMap).count(m_option_autoCorr_numLags)) {
527  m_autoCorrNumLags = (*m_optionsMap)[m_option_autoCorr_numLags].as<unsigned int>();
528  }
529 
530  if ((*m_optionsMap).count(m_option_autoCorr_display)) {
531  m_autoCorrDisplay = (*m_optionsMap)[m_option_autoCorr_display].as<bool>();
532  }
533 
534  if ((*m_optionsMap).count(m_option_autoCorr_write)) {
535  m_autoCorrWrite = (*m_optionsMap)[m_option_autoCorr_write].as<bool>();
536  }
537 
538  if ((*m_optionsMap).count(m_option_kde_compute)) {
539  m_kdeCompute = (*m_optionsMap)[m_option_kde_compute].as<bool>();
540  }
541 
542  if ((*m_optionsMap).count(m_option_kde_numEvalPositions)) {
543  m_kdeNumEvalPositions = (*m_optionsMap)[m_option_kde_numEvalPositions].as<unsigned int>();
544  }
545 
546  if ((*m_optionsMap).count(m_option_covMatrix_compute)) {
547  m_covMatrixCompute = (*m_optionsMap)[m_option_covMatrix_compute].as<bool>();
548  }
549 
550  if ((*m_optionsMap).count(m_option_corrMatrix_compute)) {
551  m_corrMatrixCompute = (*m_optionsMap)[m_option_corrMatrix_compute].as<bool>();
552  }
553 }
554 
555 void
556 SsOptionsValues::copy(const SsOptionsValues& src)
557 {
558  m_initialDiscardedPortions = src.m_initialDiscardedPortions;
559 #ifdef QUESO_COMPUTES_EXTRA_POST_PROCESSING_STATISTICS
560  m_meanMonitorPeriod = src.m_meanMonitorPeriod;
561  m_bmmRun = src.m_bmmRun;
562  m_bmmLengths = src.m_bmmLengths;
563  m_fftCompute = src.m_fftCompute;
564  m_fftParamId = src.m_fftParamId;
565  m_fftSize = src.m_fftSize;
566  m_fftTestInversion = src.m_fftTestInversion;
567  m_fftWrite = src.m_fftWrite;
568  m_psdCompute = src.m_psdCompute;
569  m_psdNumBlocks = src.m_psdNumBlocks;
570  m_psdHopSizeRatio = src.m_psdHopSizeRatio;
571  m_psdParamId = src.m_psdParamId;
572  m_psdWrite = src.m_psdWrite;
573  m_psdAtZeroCompute = src.m_psdAtZeroCompute;
574  m_psdAtZeroNumBlocks = src.m_psdAtZeroNumBlocks;
575  m_psdAtZeroHopSizeRatio = src.m_psdAtZeroHopSizeRatio;
576  m_psdAtZeroDisplay = src.m_psdAtZeroDisplay;
577  m_psdAtZeroWrite = src.m_psdAtZeroWrite;
578  m_gewekeCompute = src.m_gewekeCompute;
579  m_gewekeNaRatio = src.m_gewekeNaRatio;
580  m_gewekeNbRatio = src.m_gewekeNbRatio;
581  m_gewekeDisplay = src.m_gewekeDisplay;
582  m_gewekeWrite = src.m_gewekeWrite;
583  m_meanStaccCompute = src.m_meanStaccCompute;
584  m_histCompute = src.m_histCompute;
585  m_histNumInternalBins = src.m_histNumInternalBins;
586  m_cdfStaccCompute = src.m_cdfStaccCompute;
587  m_cdfStaccNumEvalPositions = src.m_cdfStaccNumEvalPositions;
588 #endif
589  m_autoCorrComputeViaDef = src.m_autoCorrComputeViaDef;
590  m_autoCorrComputeViaFft = src.m_autoCorrComputeViaFft;
591  m_autoCorrSecondLag = src.m_autoCorrSecondLag;
592  m_autoCorrLagSpacing = src.m_autoCorrLagSpacing;
593  m_autoCorrNumLags = src.m_autoCorrNumLags;
594  m_autoCorrDisplay = src.m_autoCorrDisplay;
595  m_autoCorrWrite = src.m_autoCorrWrite;
596  m_kdeCompute = src.m_kdeCompute;
597  m_kdeNumEvalPositions = src.m_kdeNumEvalPositions;
598  m_covMatrixCompute = src.m_covMatrixCompute;
599  m_corrMatrixCompute = src.m_corrMatrixCompute;
600 
601  return;
602 }
603 
604 SequenceStatisticalOptions::SequenceStatisticalOptions( const BaseEnvironment& env, const std::string& prefix)
607  :
608  m_ov (),
609  m_prefix ((std::string)(prefix) + "stats_"),
610  m_env (env),
611  m_optionsDesc (new boost::program_options::options_description("Chain statistical options")),
612  m_option_help (m_prefix + "help" ),
613  m_option_initialDiscardedPortions (m_prefix + "initialDiscardedPortions" ),
614 #ifdef QUESO_COMPUTES_EXTRA_POST_PROCESSING_STATISTICS
615  m_option_mean_monitorPeriod (m_prefix + "mean_monitorPeriod" ),
616  m_option_bmm_run (m_prefix + "bmm_run" ),
617  m_option_bmm_lengths (m_prefix + "bmm_lengths" ),
618  m_option_bmm_display (m_prefix + "bmm_display" ),
619  m_option_bmm_write (m_prefix + "bmm_write" ),
620  m_option_fft_compute (m_prefix + "fft_compute" ),
621  m_option_fft_paramId (m_prefix + "fft_paramId" ),
622  m_option_fft_size (m_prefix + "fft_size" ),
623  m_option_fft_testInversion (m_prefix + "fft_testInversion" ),
624  m_option_fft_write (m_prefix + "fft_write" ),
625  m_option_psd_compute (m_prefix + "psd_compute" ),
626  m_option_psd_numBlocks (m_prefix + "psd_numBlocks" ),
627  m_option_psd_hopSizeRatio (m_prefix + "psd_hopSizeRatio" ),
628  m_option_psd_paramId (m_prefix + "psd_paramId" ),
629  m_option_psd_write (m_prefix + "psd_write" ),
630  m_option_psdAtZero_compute (m_prefix + "psdAtZero_compute" ),
631  m_option_psdAtZero_numBlocks (m_prefix + "psdAtZero_numBlocks" ),
632  m_option_psdAtZero_hopSizeRatio (m_prefix + "psdAtZero_hopSizeRatio" ),
633  m_option_psdAtZero_display (m_prefix + "psdAtZero_display" ),
634  m_option_psdAtZero_write (m_prefix + "psdAtZero_write" ),
635  m_option_geweke_compute (m_prefix + "geweke_compute" ),
636  m_option_geweke_naRatio (m_prefix + "geweke_naRatio" ),
637  m_option_geweke_nbRatio (m_prefix + "geweke_nbRatio" ),
638  m_option_geweke_display (m_prefix + "geweke_display" ),
639  m_option_geweke_write (m_prefix + "geweke_write" ),
640  m_option_meanStacc_compute (m_prefix + "meanStacc_compute" ),
641  m_option_hist_compute (m_prefix + "hist_compute" ),
642  m_option_hist_numInternalBins (m_prefix + "hist_numInternalBins" ),
643  m_option_cdfStacc_compute (m_prefix + "cdfStacc_compute" ),
644  m_option_cdfStacc_numEvalPositions(m_prefix + "cdfStacc_numEvalPositions"),
645 #endif
646  m_option_autoCorr_computeViaDef (m_prefix + "autoCorr_computeViaDef" ),
647  m_option_autoCorr_computeViaFft (m_prefix + "autoCorr_computeViaFft" ),
648  m_option_autoCorr_secondLag (m_prefix + "autoCorr_secondLag" ),
649  m_option_autoCorr_lagSpacing (m_prefix + "autoCorr_lagSpacing" ),
650  m_option_autoCorr_numLags (m_prefix + "autoCorr_numLags" ),
651  m_option_autoCorr_display (m_prefix + "autoCorr_display" ),
652  m_option_autoCorr_write (m_prefix + "autoCorr_write" ),
653  m_option_kde_compute (m_prefix + "kde_compute" ),
654  m_option_kde_numEvalPositions (m_prefix + "kde_numEvalPositions" ),
655  m_option_covMatrix_compute (m_prefix + "covMatrix_compute" ),
656  m_option_corrMatrix_compute (m_prefix + "corrMatrix_compute" )
657 {
658  queso_deprecated();
659 
660  if (m_env.subDisplayFile()) {
661  *m_env.subDisplayFile() << "Entering SequenceStatisticalOptions::constructor(1)"
662  << ", prefix = " << m_prefix
663  << std::endl;
664  }
665 
666  queso_require_not_equal_to_msg(m_env.optionsInputFileName(), "", "this constructor is incompatible with the abscense of an options input file");
667 
668  defineMyOptions (*m_optionsDesc);
669  m_env.scanInputFileForMyOptions(*m_optionsDesc);
670  getMyOptionValues (*m_optionsDesc);
671 
672  if (m_env.subDisplayFile()) {
673  *m_env.subDisplayFile() << "After reading values of options with prefix '" << m_prefix
674  << "', state of SequenceStatisticalOptions object is:"
675  << "\n" << *this
676  << std::endl;
677  }
678 
679  if (m_env.subDisplayFile()) {
680  *m_env.subDisplayFile() << "Leaving SequenceStatisticalOptions::constructor(1)"
681  << ", prefix = " << m_prefix
682  << std::endl;
683  }
684 }
685 
686 SequenceStatisticalOptions::SequenceStatisticalOptions( const BaseEnvironment& env, const std::string& prefix,
689  const SsOptionsValues& alternativeOptionsValues)
690  :
691  m_ov (alternativeOptionsValues),
692  m_prefix ((std::string)(prefix) + "stats_"),
693  m_env (env),
694  m_optionsDesc (NULL),
695  m_option_help (m_prefix + "help" ),
696  m_option_initialDiscardedPortions (m_prefix + "initialDiscardedPortions" ),
697 #ifdef QUESO_COMPUTES_EXTRA_POST_PROCESSING_STATISTICS
698  m_option_mean_monitorPeriod (m_prefix + "mean_monitorPeriod" ),
699  m_option_bmm_run (m_prefix + "bmm_run" ),
700  m_option_bmm_lengths (m_prefix + "bmm_lengths" ),
701  m_option_bmm_display (m_prefix + "bmm_display" ),
702  m_option_bmm_write (m_prefix + "bmm_write" ),
703  m_option_fft_compute (m_prefix + "fft_compute" ),
704  m_option_fft_paramId (m_prefix + "fft_paramId" ),
705  m_option_fft_size (m_prefix + "fft_size" ),
706  m_option_fft_testInversion (m_prefix + "fft_testInversion" ),
707  m_option_fft_write (m_prefix + "fft_write" ),
708  m_option_psd_compute (m_prefix + "psd_compute" ),
709  m_option_psd_numBlocks (m_prefix + "psd_numBlocks" ),
710  m_option_psd_hopSizeRatio (m_prefix + "psd_hopSizeRatio" ),
711  m_option_psd_paramId (m_prefix + "psd_paramId" ),
712  m_option_psd_write (m_prefix + "psd_write" ),
713  m_option_psdAtZero_compute (m_prefix + "psdAtZero_compute" ),
714  m_option_psdAtZero_numBlocks (m_prefix + "psdAtZero_numBlocks" ),
715  m_option_psdAtZero_hopSizeRatio (m_prefix + "psdAtZero_hopSizeRatio" ),
716  m_option_psdAtZero_display (m_prefix + "psdAtZero_display" ),
717  m_option_psdAtZero_write (m_prefix + "psdAtZero_write" ),
718  m_option_geweke_compute (m_prefix + "geweke_compute" ),
719  m_option_geweke_naRatio (m_prefix + "geweke_naRatio" ),
720  m_option_geweke_nbRatio (m_prefix + "geweke_nbRatio" ),
721  m_option_geweke_display (m_prefix + "geweke_display" ),
722  m_option_geweke_write (m_prefix + "geweke_write" ),
723  m_option_meanStacc_compute (m_prefix + "meanStacc_compute" ),
724  m_option_hist_compute (m_prefix + "hist_compute" ),
725  m_option_hist_numInternalBins (m_prefix + "hist_numInternalBins" ),
726  m_option_cdfStacc_compute (m_prefix + "cdfStacc_compute" ),
727  m_option_cdfStacc_numEvalPositions(m_prefix + "cdfStacc_numEvalPositions"),
728 #endif
729  m_option_autoCorr_computeViaDef (m_prefix + "autoCorr_computeViaDef" ),
730  m_option_autoCorr_computeViaFft (m_prefix + "autoCorr_computeViaFft" ),
731  m_option_autoCorr_secondLag (m_prefix + "autoCorr_secondLag" ),
732  m_option_autoCorr_lagSpacing (m_prefix + "autoCorr_lagSpacing" ),
733  m_option_autoCorr_numLags (m_prefix + "autoCorr_numLags" ),
734  m_option_autoCorr_display (m_prefix + "autoCorr_display" ),
735  m_option_autoCorr_write (m_prefix + "autoCorr_write" ),
736  m_option_kde_compute (m_prefix + "kde_compute" ),
737  m_option_kde_numEvalPositions (m_prefix + "kde_numEvalPositions" ),
738  m_option_covMatrix_compute (m_prefix + "covMatrix_compute" ),
739  m_option_corrMatrix_compute (m_prefix + "corrMatrix_compute" )
740 {
741  queso_deprecated();
742 
743  if (m_env.subDisplayFile()) {
744  *m_env.subDisplayFile() << "Entering SequenceStatisticalOptions::constructor(2)"
745  << ", prefix = " << m_prefix
746  << std::endl;
747  }
748 
749  queso_require_equal_to_msg(m_env.optionsInputFileName(), "", "this constructor is incompatible with the existence of an options input file");
750 
751  if (m_env.subDisplayFile()) {
752  *m_env.subDisplayFile() << "After setting values of options with prefix '" << m_prefix
753  << "', state of SequenceStatisticalOptions object is:"
754  << "\n" << *this
755  << std::endl;
756  }
757 
758  if (m_env.subDisplayFile()) {
759  *m_env.subDisplayFile() << "Leaving SequenceStatisticalOptions::constructor(2)"
760  << ", prefix = " << m_prefix
761  << std::endl;
762  }
763 }
764 
765 SequenceStatisticalOptions::~SequenceStatisticalOptions()
766 {
767  queso_deprecated();
768 
769  if (m_optionsDesc) delete m_optionsDesc;
770 }
771 
772 void
773 SequenceStatisticalOptions::defineMyOptions(
774  boost::program_options::options_description& optionsDesc) const
775 {
776  queso_deprecated();
777 
778  optionsDesc.add_options()
779  (m_option_help.c_str(), "produce help message for chain statistical options" )
780  (m_option_initialDiscardedPortions.c_str(), boost::program_options::value<std::string >()->default_value(UQ_SEQUENCE_INITIAL_DISCARDED_PORTIONS_ODV ), "list of initial discarded portions for chain statistics" )
781 #ifdef QUESO_COMPUTES_EXTRA_POST_PROCESSING_STATISTICS
782  (m_option_mean_monitorPeriod.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_MEAN_MONITOR_PERIOD_ODV ), "period for monitoring mean" )
783  (m_option_bmm_run.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_BMM_RUN_ODV ), "compute variance of sample mean with batch means method" )
784  (m_option_bmm_lengths.c_str(), boost::program_options::value<std::string >()->default_value(UQ_SEQUENCE_BMM_LENGTHS_ODV ), "list of batch lenghts for BMM" )
785  (m_option_fft_compute.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_FFT_COMPUTE_ODV ), "compute fft" )
786  (m_option_fft_paramId.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_FFT_PARAM_ID_ODV ), "parameter id for fft computations" )
787  (m_option_fft_size.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_FFT_SIZE_ODV ), "fft size" )
788  (m_option_fft_testInversion.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_FFT_TEST_INVERSION_ODV ), "test fft inversion" )
789  (m_option_fft_write.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_FFT_WRITE_ODV ), "write fft" )
790  (m_option_psd_compute.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_PSD_COMPUTE_ODV ), "compute psd" )
791  (m_option_psd_numBlocks.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_PSD_NUM_BLOCKS_ODV ), "number of blocks for computation of psd" )
792  (m_option_psd_hopSizeRatio.c_str(), boost::program_options::value<double >()->default_value(UQ_SEQUENCE_PSD_HOP_SIZE_RATIO_ODV ), "hop size ratio for psd" )
793  (m_option_psd_paramId.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_PSD_PARAM_ID_ODV ), "parameter id for psd computations" )
794  (m_option_psd_write.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_PSD_WRITE_ODV ), "write psd" )
795  (m_option_psdAtZero_compute.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_PSD_AT_ZERO_COMPUTE_ODV ), "compute power spectral densities" )
796  (m_option_psdAtZero_numBlocks.c_str(), boost::program_options::value<std::string >()->default_value(UQ_SEQUENCE_PSD_AT_ZERO_NUM_BLOCKS_ODV ), "list of numbers of blocks for computation of psd at zero" )
797  (m_option_psdAtZero_hopSizeRatio.c_str(), boost::program_options::value<double >()->default_value(UQ_SEQUENCE_PSD_AT_ZERO_HOP_SIZE_RATIO_ODV ), "hop size ratio for psd at zero" )
798  (m_option_psdAtZero_display.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_PSD_AT_ZERO_DISPLAY_ODV ), "display computed psd at frequency zero on screen" )
799  (m_option_psdAtZero_write.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_PSD_AT_ZERO_WRITE_ODV ), "write computed psd at frequency zero to the output file" )
800  (m_option_geweke_compute.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_GEWEKE_COMPUTE_ODV ), "compute Geweke coefficients" )
801  (m_option_geweke_naRatio.c_str(), boost::program_options::value<double >()->default_value(UQ_SEQUENCE_GEWEKE_NA_RATIO_ODV ), "ratio NA for Geweke" )
802  (m_option_geweke_nbRatio.c_str(), boost::program_options::value<double >()->default_value(UQ_SEQUENCE_GEWEKE_NB_RATIO_ODV ), "ratio NB for Geweke" )
803  (m_option_geweke_display.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_GEWEKE_DISPLAY_ODV ), "display computed Geweke on screen" )
804  (m_option_geweke_write.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_GEWEKE_WRITE_ODV ), "write computed Geweke to the output file" )
805  (m_option_meanStacc_compute.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_MEAN_STACC_COMPUTE_ODV ), "compute statistical accuracy of mean" )
806  (m_option_hist_compute.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_HIST_COMPUTE_ODV ), "compute histograms" )
807  (m_option_hist_numInternalBins.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_HIST_NUM_INTERNAL_BINS_ODV ), "number of internal bins" )
808  (m_option_cdfStacc_compute.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_CDF_STACC_COMPUTE_ODV ), "compute statisical accuracy of cdf" )
809  (m_option_cdfStacc_numEvalPositions.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_CDF_STACC_NUM_EVAL_POSITIONS_ODV ), "number of evaluations points for statistical accuracy of cdf" )
810 #endif
811  (m_option_autoCorr_computeViaDef.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_AUTO_CORR_COMPUTE_VIA_DEF_ODV ), "compute correlations via definition" )
812  (m_option_autoCorr_computeViaFft.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_AUTO_CORR_COMPUTE_VIA_FFT_ODV ), "compute correlations via fft" )
813  (m_option_autoCorr_secondLag.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_AUTO_CORR_SECOND_LAG_ODV ), "second lag for computation of autocorrelations" )
814  (m_option_autoCorr_lagSpacing.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_AUTO_CORR_LAG_SPACING_ODV ), "lag spacing for computation of autocorrelations" )
815  (m_option_autoCorr_numLags.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_AUTO_CORR_NUM_LAGS_ODV ), "number of lags for computation of autocorrelations" )
816  (m_option_autoCorr_display.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_AUTO_CORR_DISPLAY_ODV ), "display computed autocorrelations on the screen" )
817  (m_option_autoCorr_write.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_AUTO_CORR_WRITE_ODV ), "write computed autocorrelations to the output file" )
818  (m_option_kde_compute.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_KDE_COMPUTE_ODV ), "compute kernel density estimators" )
819  (m_option_kde_numEvalPositions.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_SEQUENCE_KDE_NUM_EVAL_POSITIONS_ODV ), "number of evaluation positions" )
820  (m_option_covMatrix_compute.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_COV_MATRIX_COMPUTE_ODV ), "compute covariance matrix" )
821  (m_option_corrMatrix_compute.c_str(), boost::program_options::value<bool >()->default_value(UQ_SEQUENCE_CORR_MATRIX_COMPUTE_ODV ), "compute correlation matrix" )
822  ;
823 
824  return;
825 }
826 
827 void
828 SequenceStatisticalOptions::getMyOptionValues(
829  boost::program_options::options_description& optionsDesc)
830 {
831  queso_deprecated();
832 
833  if (m_env.allOptionsMap().count(m_option_help)) {
834  if (m_env.subDisplayFile()) {
835  *m_env.subDisplayFile() << optionsDesc
836  << std::endl;
837  }
838  }
839 
840  if (m_env.allOptionsMap().count(m_option_initialDiscardedPortions)) {
841  m_ov.m_initialDiscardedPortions.clear();
842  std::vector<double> tmpPortions(0,0.);
843  std::string inputString = m_env.allOptionsMap()[m_option_initialDiscardedPortions].as<std::string>();
844  MiscReadDoublesFromString(inputString,tmpPortions);
845  //if (m_env.subDisplayFile()) {
846  // *m_env.subDisplayFile() << "In SequenceStatisticalOptions::getMyOptionValues(): percents = ";
847  // for (unsigned int i = 0; i < tmpPortions.size(); ++i) {
848  // *m_env.subDisplayFile() << " " << tmpPortions[i];
849  // }
850  // *m_env.subDisplayFile() << std::endl;
851  //}
852 
853  if (tmpPortions.size() > 0) {
854  m_ov.m_initialDiscardedPortions.resize(tmpPortions.size(),0.);
855  for (unsigned int i = 0; i < m_ov.m_initialDiscardedPortions.size(); ++i) {
856  m_ov.m_initialDiscardedPortions[i] = tmpPortions[i];
857  }
858  }
859  }
860 
861 #ifdef QUESO_COMPUTES_EXTRA_POST_PROCESSING_STATISTICS
862  if (m_env.allOptionsMap().count(m_option_mean_monitorPeriod)) {
863  m_ov.m_meanMonitorPeriod = m_env.allOptionsMap()[m_option_mean_monitorPeriod].as<unsigned int>();
864  }
865 
866  if (m_env.allOptionsMap().count(m_option_bmm_run)) {
867  m_ov.m_bmmRun = m_env.allOptionsMap()[m_option_bmm_run].as<bool>();
868  }
869 
870  if (m_env.allOptionsMap().count(m_option_bmm_lengths)) {
871  m_ov.m_bmmLengths.clear();
872  std::vector<double> tmpLengths(0,0.);
873  std::string inputString = m_env.allOptionsMap()[m_option_bmm_lengths].as<std::string>();
874  MiscReadDoublesFromString(inputString,tmpLengths);
875  //if (m_env.subDisplayFile()) {
876  // *m_env.subDisplayFile() << "In SequenceStatisticalOptions::getMyOptionValues(): lengths for BMM = ";
877  // for (unsigned int i = 0; i < tmpLengths.size(); ++i) {
878  // *m_env.subDisplayFile() << " " << tmpLengths[i];
879  // }
880  // *m_env.subDisplayFile() << std::endl;
881  //}
882 
883  if (tmpLengths.size() > 0) {
884  m_ov.m_bmmLengths.resize(tmpLengths.size(),0);
885  for (unsigned int i = 0; i < m_ov.m_bmmLengths.size(); ++i) {
886  m_ov.m_bmmLengths[i] = (unsigned int) tmpLengths[i];
887  }
888  }
889  }
890 
891  if (m_env.allOptionsMap().count(m_option_fft_compute)) {
892  m_ov.m_fftCompute = m_env.allOptionsMap()[m_option_fft_compute].as<bool>();
893  }
894 
895  if (m_env.allOptionsMap().count(m_option_fft_paramId)) {
896  m_ov.m_fftParamId = m_env.allOptionsMap()[m_option_fft_paramId].as<unsigned int>();
897  }
898 
899  if (m_env.allOptionsMap().count(m_option_fft_size)) {
900  m_ov.m_fftSize = m_env.allOptionsMap()[m_option_fft_size].as<unsigned int>();
901  }
902 
903  if (m_env.allOptionsMap().count(m_option_fft_testInversion)) {
904  m_ov.m_fftTestInversion = m_env.allOptionsMap()[m_option_fft_testInversion].as<bool>();
905  }
906 
907  if (m_env.allOptionsMap().count(m_option_fft_write)) {
908  m_ov.m_fftWrite = m_env.allOptionsMap()[m_option_fft_write].as<bool>();
909  }
910 
911  if (m_env.allOptionsMap().count(m_option_psd_compute)) {
912  m_ov.m_psdCompute = m_env.allOptionsMap()[m_option_psd_compute].as<bool>();
913  }
914 
915  if (m_env.allOptionsMap().count(m_option_psd_numBlocks)) {
916  m_ov.m_psdNumBlocks = m_env.allOptionsMap()[m_option_psd_numBlocks].as<unsigned int>();
917  }
918 
919  if (m_env.allOptionsMap().count(m_option_psd_hopSizeRatio)) {
920  m_ov.m_psdHopSizeRatio = m_env.allOptionsMap()[m_option_psd_hopSizeRatio].as<double>();
921  }
922 
923  if (m_env.allOptionsMap().count(m_option_psd_paramId)) {
924  m_ov.m_psdParamId = m_env.allOptionsMap()[m_option_psd_paramId].as<unsigned int>();
925  }
926 
927  if (m_env.allOptionsMap().count(m_option_psd_write)) {
928  m_ov.m_psdWrite = m_env.allOptionsMap()[m_option_psd_write].as<bool>();
929  }
930 
931  if (m_env.allOptionsMap().count(m_option_psdAtZero_compute)) {
932  m_ov.m_psdAtZeroCompute = m_env.allOptionsMap()[m_option_psdAtZero_compute].as<bool>();
933  }
934 
935  if (m_env.allOptionsMap().count(m_option_psdAtZero_numBlocks)) {
936  m_ov.m_psdAtZeroNumBlocks.clear();
937  std::vector<double> tmpNumBlocks(0,0.);
938  std::string inputString = m_env.allOptionsMap()[m_option_psdAtZero_numBlocks].as<std::string>();
939  MiscReadDoublesFromString(inputString,tmpNumBlocks);
940  //if (m_env.subDisplayFile()) {
941  // *m_env.subDisplayFile() << "In SequenceStatisticalOptions::getMyOptionValues(): numBlocks for psdAtZero = ";
942  // for (unsigned int i = 0; i < tmpNumBlocks.size(); ++i) {
943  // *m_env.subDisplayFile() << " " << numBlocks[i];
944  // }
945  // *m_env.subDisplayFile() << std::endl;
946  //}
947 
948  if (tmpNumBlocks.size() > 0) {
949  m_ov.m_psdAtZeroNumBlocks.resize(tmpNumBlocks.size(),0);
950  for (unsigned int i = 0; i < m_ov.m_psdAtZeroNumBlocks.size(); ++i) {
951  m_ov.m_psdAtZeroNumBlocks[i] = (unsigned int) tmpNumBlocks[i];
952  }
953  }
954  }
955 
956  if (m_env.allOptionsMap().count(m_option_psdAtZero_hopSizeRatio)) {
957  m_ov.m_psdAtZeroHopSizeRatio = m_env.allOptionsMap()[m_option_psdAtZero_hopSizeRatio].as<double>();
958  }
959 
960  if (m_env.allOptionsMap().count(m_option_psdAtZero_display)) {
961  m_ov.m_psdAtZeroDisplay = m_env.allOptionsMap()[m_option_psdAtZero_display].as<bool>();
962  }
963 
964  if (m_env.allOptionsMap().count(m_option_psdAtZero_write)) {
965  m_ov.m_psdAtZeroWrite = m_env.allOptionsMap()[m_option_psdAtZero_write].as<bool>();
966  }
967 
968  if (m_env.allOptionsMap().count(m_option_geweke_compute)) {
969  m_ov.m_gewekeCompute = m_env.allOptionsMap()[m_option_geweke_compute].as<bool>();
970  }
971 
972  if (m_env.allOptionsMap().count(m_option_geweke_naRatio)) {
973  m_ov.m_gewekeNaRatio = m_env.allOptionsMap()[m_option_geweke_naRatio].as<double>();
974  }
975 
976  if (m_env.allOptionsMap().count(m_option_geweke_nbRatio)) {
977  m_ov.m_gewekeNbRatio = m_env.allOptionsMap()[m_option_geweke_nbRatio].as<double>();
978  }
979 
980  if (m_env.allOptionsMap().count(m_option_geweke_display)) {
981  m_ov.m_gewekeDisplay = m_env.allOptionsMap()[m_option_geweke_display].as<bool>();
982  }
983 
984  if (m_env.allOptionsMap().count(m_option_geweke_write)) {
985  m_ov.m_gewekeWrite = m_env.allOptionsMap()[m_option_geweke_write].as<bool>();
986  }
987 
988  if (m_env.allOptionsMap().count(m_option_meanStacc_compute)) {
989  m_ov.m_meanStaccCompute = m_env.allOptionsMap()[m_option_meanStacc_compute].as<bool>();
990  }
991 
992  if (m_env.allOptionsMap().count(m_option_hist_compute)) {
993  m_ov.m_histCompute = m_env.allOptionsMap()[m_option_hist_compute].as<bool>();
994  }
995 
996  if (m_env.allOptionsMap().count(m_option_hist_numInternalBins)) {
997  m_ov.m_histNumInternalBins = m_env.allOptionsMap()[m_option_hist_numInternalBins].as<unsigned int>();
998  }
999 
1000  if (m_env.allOptionsMap().count(m_option_cdfStacc_compute)) {
1001  m_ov.m_cdfStaccCompute = m_env.allOptionsMap()[m_option_cdfStacc_compute].as<bool>();
1002  }
1003 
1004  if (m_env.allOptionsMap().count(m_option_cdfStacc_numEvalPositions)) {
1005  m_ov.m_cdfStaccNumEvalPositions = m_env.allOptionsMap()[m_option_cdfStacc_numEvalPositions].as<unsigned int>();
1006  }
1007 #endif
1008  if (m_env.allOptionsMap().count(m_option_autoCorr_computeViaDef)) {
1009  m_ov.m_autoCorrComputeViaDef = m_env.allOptionsMap()[m_option_autoCorr_computeViaDef].as<bool>();
1010  }
1011 
1012  if (m_env.allOptionsMap().count(m_option_autoCorr_computeViaFft)) {
1013  m_ov.m_autoCorrComputeViaFft = m_env.allOptionsMap()[m_option_autoCorr_computeViaFft].as<bool>();
1014  }
1015 
1016  if (m_env.allOptionsMap().count(m_option_autoCorr_secondLag)) {
1017  m_ov.m_autoCorrSecondLag = m_env.allOptionsMap()[m_option_autoCorr_secondLag].as<unsigned int>();
1018  }
1019 
1020  if (m_env.allOptionsMap().count(m_option_autoCorr_lagSpacing)) {
1021  m_ov.m_autoCorrLagSpacing = m_env.allOptionsMap()[m_option_autoCorr_lagSpacing].as<unsigned int>();
1022  }
1023 
1024  if (m_env.allOptionsMap().count(m_option_autoCorr_numLags)) {
1025  m_ov.m_autoCorrNumLags = m_env.allOptionsMap()[m_option_autoCorr_numLags].as<unsigned int>();
1026  }
1027 
1028  if (m_env.allOptionsMap().count(m_option_autoCorr_display)) {
1029  m_ov.m_autoCorrDisplay = m_env.allOptionsMap()[m_option_autoCorr_display].as<bool>();
1030  }
1031 
1032  if (m_env.allOptionsMap().count(m_option_autoCorr_write)) {
1033  m_ov.m_autoCorrWrite = m_env.allOptionsMap()[m_option_autoCorr_write].as<bool>();
1034  }
1035 
1036  if (m_env.allOptionsMap().count(m_option_kde_compute)) {
1037  m_ov.m_kdeCompute = m_env.allOptionsMap()[m_option_kde_compute].as<bool>();
1038  }
1039 
1040  if (m_env.allOptionsMap().count(m_option_kde_numEvalPositions)) {
1041  m_ov.m_kdeNumEvalPositions = m_env.allOptionsMap()[m_option_kde_numEvalPositions].as<unsigned int>();
1042  }
1043 
1044  if (m_env.allOptionsMap().count(m_option_covMatrix_compute)) {
1045  m_ov.m_covMatrixCompute = m_env.allOptionsMap()[m_option_covMatrix_compute].as<bool>();
1046  }
1047 
1048  if (m_env.allOptionsMap().count(m_option_corrMatrix_compute)) {
1049  m_ov.m_corrMatrixCompute = m_env.allOptionsMap()[m_option_corrMatrix_compute].as<bool>();
1050  }
1051 
1052  return;
1053 }
1054 
1055 const std::vector<double>&
1056 SequenceStatisticalOptions::initialDiscardedPortions() const
1057 {
1058  queso_deprecated();
1059 
1060  return m_ov.m_initialDiscardedPortions;
1061 }
1062 
1063 #ifdef QUESO_COMPUTES_EXTRA_POST_PROCESSING_STATISTICS
1064 unsigned int
1065 SequenceStatisticalOptions::meanMonitorPeriod() const
1066 {
1067  queso_deprecated();
1068 
1069  return m_ov.m_meanMonitorPeriod;
1070 }
1071 
1072 bool
1073 SequenceStatisticalOptions::bmmRun() const
1074 {
1075  queso_deprecated();
1076 
1077  return m_ov.m_bmmRun;
1078 }
1079 
1080 const std::vector<unsigned int>&
1081 SequenceStatisticalOptions::bmmLengths() const
1082 {
1083  queso_deprecated();
1084 
1085  return m_ov.m_bmmLengths;
1086 }
1087 
1088 bool
1089 SequenceStatisticalOptions::bmmDisplay() const
1090 {
1091  queso_deprecated();
1092 
1093  return m_ov.m_bmmDisplay;
1094 }
1095 
1096 bool
1097 SequenceStatisticalOptions::bmmWrite() const
1098 {
1099  queso_deprecated();
1100 
1101  return m_ov.m_bmmWrite;
1102 }
1103 
1104 bool
1105 SequenceStatisticalOptions::fftCompute() const
1106 {
1107  queso_deprecated();
1108 
1109  return m_ov.m_fftCompute;
1110 }
1111 
1112 unsigned int
1113 SequenceStatisticalOptions::fftParamId() const
1114 {
1115  queso_deprecated();
1116 
1117  return m_ov.m_fftParamId;
1118 }
1119 
1120 unsigned int
1121 SequenceStatisticalOptions::fftSize() const
1122 {
1123  queso_deprecated();
1124 
1125  return m_ov.m_fftSize;
1126 }
1127 
1128 bool
1129 SequenceStatisticalOptions::fftTestInversion() const
1130 {
1131  queso_deprecated();
1132 
1133  return m_ov.m_fftTestInversion;
1134 }
1135 
1136 bool
1137 SequenceStatisticalOptions::fftWrite() const
1138 {
1139  queso_deprecated();
1140 
1141  return m_ov.m_fftWrite;
1142 }
1143 
1144 bool
1145 SequenceStatisticalOptions::psdCompute() const
1146 {
1147  queso_deprecated();
1148 
1149  return m_ov.m_psdCompute;
1150 }
1151 
1152 unsigned int
1153 SequenceStatisticalOptions::psdNumBlocks() const
1154 {
1155  queso_deprecated();
1156 
1157  return m_ov.m_psdNumBlocks;
1158 }
1159 
1160 double
1161 SequenceStatisticalOptions::psdHopSizeRatio() const
1162 {
1163  queso_deprecated();
1164 
1165  return m_ov.m_psdHopSizeRatio;
1166 }
1167 
1168 unsigned int
1169 SequenceStatisticalOptions::psdParamId() const
1170 {
1171  queso_deprecated();
1172 
1173  return m_ov.m_psdParamId;
1174 }
1175 
1176 bool
1177 SequenceStatisticalOptions::psdWrite() const
1178 {
1179  queso_deprecated();
1180 
1181  return m_ov.m_psdWrite;
1182 }
1183 
1184 bool
1185 SequenceStatisticalOptions::psdAtZeroCompute() const
1186 {
1187  queso_deprecated();
1188 
1189  return m_ov.m_psdAtZeroCompute;
1190 }
1191 
1192 const std::vector<unsigned int>&
1193 SequenceStatisticalOptions::psdAtZeroNumBlocks() const
1194 {
1195  queso_deprecated();
1196 
1197  return m_ov.m_psdAtZeroNumBlocks;
1198 }
1199 
1200 double
1201 SequenceStatisticalOptions::psdAtZeroHopSizeRatio() const
1202 {
1203  queso_deprecated();
1204 
1205  return m_ov.m_psdAtZeroHopSizeRatio;
1206 }
1207 
1208 bool
1209 SequenceStatisticalOptions::psdAtZeroDisplay() const
1210 {
1211  queso_deprecated();
1212 
1213  return m_ov.m_psdAtZeroDisplay;
1214 }
1215 
1216 bool
1217 SequenceStatisticalOptions::psdAtZeroWrite() const
1218 {
1219  queso_deprecated();
1220 
1221  return m_ov.m_psdAtZeroWrite;
1222 }
1223 
1224 bool
1225 SequenceStatisticalOptions::gewekeCompute() const
1226 {
1227  queso_deprecated();
1228 
1229  return m_ov.m_gewekeCompute;
1230 }
1231 
1232 double
1233 SequenceStatisticalOptions::gewekeNaRatio() const
1234 {
1235  queso_deprecated();
1236 
1237  return m_ov.m_gewekeNaRatio;
1238 }
1239 
1240 double
1241 SequenceStatisticalOptions::gewekeNbRatio() const
1242 {
1243  queso_deprecated();
1244 
1245  return m_ov.m_gewekeNbRatio;
1246 }
1247 
1248 bool
1249 SequenceStatisticalOptions::gewekeDisplay() const
1250 {
1251  queso_deprecated();
1252 
1253  return m_ov.m_gewekeDisplay;
1254 }
1255 
1256 bool
1257 SequenceStatisticalOptions::gewekeWrite() const
1258 {
1259  queso_deprecated();
1260 
1261  return m_ov.m_gewekeWrite;
1262 }
1263 
1264 bool
1265 SequenceStatisticalOptions::meanStaccCompute() const
1266 {
1267  queso_deprecated();
1268 
1269  return m_ov.m_meanStaccCompute;
1270 }
1271 
1272 bool
1273 SequenceStatisticalOptions::histCompute() const
1274 {
1275  queso_deprecated();
1276 
1277  return m_ov.m_histCompute;
1278 }
1279 
1280 unsigned int
1281 SequenceStatisticalOptions::histNumInternalBins() const
1282 {
1283  queso_deprecated();
1284 
1285  return m_ov.m_histNumInternalBins;
1286 }
1287 
1288 bool
1289 SequenceStatisticalOptions::cdfStaccCompute() const
1290 {
1291  queso_deprecated();
1292 
1293  return m_ov.m_cdfStaccCompute;
1294 }
1295 
1296 unsigned int
1297 SequenceStatisticalOptions::cdfStaccNumEvalPositions() const
1298 {
1299  queso_deprecated();
1300 
1301  return m_ov.m_cdfStaccNumEvalPositions;
1302 }
1303 #endif
1304 bool
1305 SequenceStatisticalOptions::autoCorrComputeViaDef() const
1306 {
1307  queso_deprecated();
1308 
1309  return m_ov.m_autoCorrComputeViaDef;
1310 }
1311 
1312 bool
1313 SequenceStatisticalOptions::autoCorrComputeViaFft() const
1314 {
1315  queso_deprecated();
1316 
1317  return m_ov.m_autoCorrComputeViaFft;
1318 }
1319 
1320 unsigned int
1321 SequenceStatisticalOptions::autoCorrSecondLag() const
1322 {
1323  queso_deprecated();
1324 
1325  return m_ov.m_autoCorrSecondLag;
1326 }
1327 
1328 unsigned int
1329 SequenceStatisticalOptions::autoCorrLagSpacing() const
1330 {
1331  queso_deprecated();
1332 
1333  return m_ov.m_autoCorrLagSpacing;
1334 }
1335 
1336 unsigned int
1337 SequenceStatisticalOptions::autoCorrNumLags() const
1338 {
1339  queso_deprecated();
1340 
1341  return m_ov.m_autoCorrNumLags;
1342 }
1343 
1344 bool
1345 SequenceStatisticalOptions::autoCorrDisplay() const
1346 {
1347  queso_deprecated();
1348 
1349  return m_ov.m_autoCorrDisplay;
1350 }
1351 
1352 bool
1353 SequenceStatisticalOptions::autoCorrWrite() const
1354 {
1355  queso_deprecated();
1356 
1357  return m_ov.m_autoCorrWrite;
1358 }
1359 
1360 bool
1361 SequenceStatisticalOptions::kdeCompute() const
1362 {
1363  queso_deprecated();
1364 
1365  return m_ov.m_kdeCompute;
1366 }
1367 
1368 unsigned int
1369 SequenceStatisticalOptions::kdeNumEvalPositions() const
1370 {
1371  queso_deprecated();
1372 
1373  return m_ov.m_kdeNumEvalPositions;
1374 }
1375 
1376 bool
1377 SequenceStatisticalOptions::covMatrixCompute() const
1378 {
1379  queso_deprecated();
1380 
1381  return m_ov.m_covMatrixCompute;
1382 }
1383 
1384 bool
1385 SequenceStatisticalOptions::corrMatrixCompute() const
1386 {
1387  queso_deprecated();
1388 
1389  return m_ov.m_corrMatrixCompute;
1390 }
1391 
1392 void
1393 SequenceStatisticalOptions::print(std::ostream& os) const
1394 {
1395  queso_deprecated();
1396 
1397  os << "\n" << m_option_initialDiscardedPortions << " = ";
1398  for (unsigned int i = 0; i < m_ov.m_initialDiscardedPortions.size(); ++i) {
1399  os << m_ov.m_initialDiscardedPortions[i] << " ";
1400  }
1401  os
1402 #ifdef QUESO_COMPUTES_EXTRA_POST_PROCESSING_STATISTICS
1403  << "\n" << m_option_mean_monitorPeriod << " = " << m_ov.m_meanMonitorPeriod
1404  << "\n" << m_option_bmm_run << " = " << m_ov.m_bmmRun
1405  << "\n" << m_option_bmm_lengths << " = ";
1406  for (unsigned int i = 0; i < m_ov.m_bmmLengths.size(); ++i) {
1407  os << m_ov.m_bmmLengths[i] << " ";
1408  }
1409  os << "\n" << m_option_fft_compute << " = " << m_ov.m_fftCompute
1410  << "\n" << m_option_fft_paramId << " = " << m_ov.m_fftParamId
1411  << "\n" << m_option_fft_size << " = " << m_ov.m_fftSize
1412  << "\n" << m_option_fft_testInversion << " = " << m_ov.m_fftTestInversion
1413  << "\n" << m_option_fft_write << " = " << m_ov.m_fftWrite
1414  << "\n" << m_option_psd_compute << " = " << m_ov.m_psdCompute
1415  << "\n" << m_option_psd_paramId << " = " << m_ov.m_psdParamId
1416  << "\n" << m_option_psd_numBlocks << " = " << m_ov.m_psdNumBlocks
1417  << "\n" << m_option_psd_hopSizeRatio << " = " << m_ov.m_psdHopSizeRatio
1418  << "\n" << m_option_psd_write << " = " << m_ov.m_psdWrite
1419  << "\n" << m_option_psdAtZero_compute << " = " << m_ov.m_psdAtZeroCompute
1420  << "\n" << m_option_psdAtZero_numBlocks << " = ";
1421  for (unsigned int i = 0; i < m_ov.m_psdAtZeroNumBlocks.size(); ++i) {
1422  os << m_ov.m_psdAtZeroNumBlocks[i] << " ";
1423  }
1424  os << "\n" << m_option_psdAtZero_hopSizeRatio << " = " << m_ov.m_psdAtZeroHopSizeRatio
1425  << "\n" << m_option_psdAtZero_display << " = " << m_ov.m_psdAtZeroDisplay
1426  << "\n" << m_option_psdAtZero_write << " = " << m_ov.m_psdAtZeroWrite
1427  << "\n" << m_option_geweke_compute << " = " << m_ov.m_gewekeCompute
1428  << "\n" << m_option_geweke_naRatio << " = " << m_ov.m_gewekeNaRatio
1429  << "\n" << m_option_geweke_nbRatio << " = " << m_ov.m_gewekeNbRatio
1430  << "\n" << m_option_geweke_display << " = " << m_ov.m_gewekeDisplay
1431  << "\n" << m_option_geweke_write << " = " << m_ov.m_gewekeWrite
1432  << "\n" << m_option_meanStacc_compute << " = " << m_ov.m_meanStaccCompute
1433  << "\n" << m_option_hist_compute << " = " << m_ov.m_histCompute
1434  << "\n" << m_option_hist_numInternalBins << " = " << m_ov.m_histNumInternalBins
1435  << "\n" << m_option_cdfStacc_compute << " = " << m_ov.m_cdfStaccCompute
1436  << "\n" << m_option_cdfStacc_numEvalPositions << " = " << m_ov.m_cdfStaccNumEvalPositions
1437 #endif
1438  << "\n" << m_option_autoCorr_computeViaDef << " = " << m_ov.m_autoCorrComputeViaDef
1439  << "\n" << m_option_autoCorr_computeViaFft << " = " << m_ov.m_autoCorrComputeViaFft
1440  << "\n" << m_option_autoCorr_secondLag << " = " << m_ov.m_autoCorrSecondLag
1441  << "\n" << m_option_autoCorr_lagSpacing << " = " << m_ov.m_autoCorrLagSpacing
1442  << "\n" << m_option_autoCorr_numLags << " = " << m_ov.m_autoCorrNumLags
1443  << "\n" << m_option_autoCorr_display << " = " << m_ov.m_autoCorrDisplay
1444  << "\n" << m_option_autoCorr_write << " = " << m_ov.m_autoCorrWrite
1445  << "\n" << m_option_kde_compute << " = " << m_ov.m_kdeCompute
1446  << "\n" << m_option_kde_numEvalPositions << " = " << m_ov.m_kdeNumEvalPositions
1447  << "\n" << m_option_covMatrix_compute << " = " << m_ov.m_covMatrixCompute
1448  << "\n" << m_option_corrMatrix_compute << " = " << m_ov.m_corrMatrixCompute
1449  << std::endl;
1450 
1451  return;
1452 }
1453 
1454 std::ostream&
1455 operator<<(std::ostream& os, const SequenceStatisticalOptions& obj)
1456 {
1457  queso_deprecated();
1458 
1459  obj.print(os);
1460 
1461  return os;
1462 }
1463 
1464 } // End namespace QUESO
1465 
1466 #endif // ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:431
QUESO::BaseEnvironment::scanInputFileForMyOptions
void scanInputFileForMyOptions(const boost::program_options::options_description &optionsDesc) const
This method scans the input file provided by the user to QUESO.
Definition: Environment.C:345
queso_require_not_equal_to_msg
#define queso_require_not_equal_to_msg(expr1, expr2, msg)
Definition: asserts.h:86
QUESO::operator<<
std::ostream & operator<<(std::ostream &os, const BaseEnvironment &obj)
queso_require_equal_to_msg
#define queso_require_equal_to_msg(expr1, expr2, msg)
Definition: asserts.h:85
QUESO::BaseEnvironment::optionsInputFileName
std::string optionsInputFileName() const
Access to the attribute m_optionsInputFileName, which stores the name of the input file passed by the...
Definition: Environment.C:307
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:274
QUESO::MiscReadDoublesFromString
void MiscReadDoublesFromString(const std::string &inputString, std::vector< double > &outputDoubles)
Definition: Miscellaneous.C:40
queso_deprecated
#define queso_deprecated()
Definition: Defines.h:120
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Definition: License.txt:60
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