/[escript]/trunk/escript/src/DataConstant.cpp
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revision 682 by robwdcock, Mon Mar 27 02:43:09 2006 UTC revision 2105 by jfenwick, Fri Nov 28 01:52:12 2008 UTC
# Line 1  Line 1 
 //$Id$  
 /*  
  ************************************************************  
  *          Copyright 2006 by ACcESS MNRF                   *  
  *                                                          *  
  *              http://www.access.edu.au                    *  
  *       Primary Business: Queensland, Australia            *  
  *  Licensed under the Open Software License version 3.0    *  
  *     http://www.opensource.org/licenses/osl-3.0.php       *  
  *                                                          *  
  ************************************************************  
 */  
1    
2    /*******************************************************
3    *
4    * Copyright (c) 2003-2008 by University of Queensland
5    * Earth Systems Science Computational Center (ESSCC)
6    * http://www.uq.edu.au/esscc
7    *
8    * Primary Business: Queensland, Australia
9    * Licensed under the Open Software License version 3.0
10    * http://www.opensource.org/licenses/osl-3.0.php
11    *
12    *******************************************************/
13    
14    
15    #include "Data.h"
16  #include "DataConstant.h"  #include "DataConstant.h"
17  #include "DataException.h"  #include "DataException.h"
18  #include "esysUtils/EsysAssert.h"  #include "esysUtils/EsysAssert.h"
19    
20  #include <iostream>  #include <iostream>
21  #include <boost/python/extract.hpp>  #include <boost/python/extract.hpp>
22    #ifdef USE_NETCDF
23    #include <netcdfcpp.h>
24    #endif
25    #ifdef PASO_MPI
26    #include <mpi.h>
27    #endif
28    
29    #include <boost/python/extract.hpp>
30    #include "DataMaths.h"
31    
32  using namespace std;  using namespace std;
33    using namespace boost::python;
34    
35  namespace escript {  namespace escript {
36    
37  DataConstant::DataConstant(const boost::python::numeric::array& value,  DataConstant::DataConstant(const boost::python::numeric::array& value,
38                             const FunctionSpace& what)                             const FunctionSpace& what)
39    : DataAbstract(what)    : parent(what,DataTypes::shapeFromNumArray(value))
40  {  {
41    DataArray temp(value);  //   // extract the shape of the numarray
42    //  //   DataTypes::ShapeType tempShape;
43    // copy the data in the correct format  //   for (int i=0; i < value.getrank(); i++) {
44    m_data=temp.getData();  //     tempShape.push_back(extract<int>(value.getshape()[i]));
45    //  //   }
46    // create the view of the data  
47    DataArrayView tempView(m_data,temp.getView().getShape());    // get the space for the data vector
48    setPointDataView(tempView);  //   int len = getNoValues();
49  }  //   DataVector temp_data(len, 0.0, len);
50    //   DataArrayView temp_dataView(temp_data, tempShape);
51    //   temp_dataView.copy(value);
52    
53  DataConstant::DataConstant(const DataArrayView& value,    m_data.copyFromNumArray(value,1);
                            const FunctionSpace& what)  
   : DataAbstract(what)  
 {  
54    //    //
55    
56    // copy the data in the correct format    // copy the data in the correct format
57    m_data=value.getData();  //   m_data=temp_data;
58    //    //
59    // create the view of the data    // create the view of the data
60    DataArrayView tempView(m_data,value.getShape());  //   DataArrayView tempView(m_data,temp_dataView.getShape());
61    setPointDataView(tempView);  //   setPointDataView(tempView);
62  }  }
63    
64    // DataConstant::DataConstant(const DataArrayView& value,
65    //                            const FunctionSpace& what)
66    //   : DataAbstract(what)
67    // {
68    //   //
69    //   // copy the data in the correct format
70    //   m_data=value.getData();
71    //   //
72    //   // create the view of the data
73    //   DataArrayView tempView(m_data,value.getShape());
74    //   setPointDataView(tempView);
75    // }
76    
77  DataConstant::DataConstant(const DataConstant& other)  DataConstant::DataConstant(const DataConstant& other)
78    : DataAbstract(other.getFunctionSpace())    : parent(other.getFunctionSpace(),other.getShape())
79  {  {  //
   //  
80    // copy the data in the correct format    // copy the data in the correct format
81    m_data=other.m_data;    m_data=other.m_data;
82    //    //
83    // create the view of the data  //   // create the view of the data
84    DataArrayView tempView(m_data,other.getPointDataView().getShape());  //   DataArrayView tempView(m_data,other.getPointDataView().getShape());
85    setPointDataView(tempView);  //   setPointDataView(tempView);
86  }  }
87    
88  DataConstant::DataConstant(const DataConstant& other,  DataConstant::DataConstant(const DataConstant& other,
89                             const DataArrayView::RegionType& region)                             const DataTypes::RegionType& region)
90    : DataAbstract(other.getFunctionSpace())    : parent(other.getFunctionSpace(),DataTypes::getResultSliceShape(region))
91  {  {
92    //    //
93    // get the shape of the slice to copy from    // get the shape of the slice to copy from
94    DataArrayView::ShapeType shape(DataArrayView::getResultSliceShape(region));  //   DataTypes::ShapeType shape(DataTypes::getResultSliceShape(region));
95    //    //
96    // allocate space for this new DataConstant's data    // allocate space for this new DataConstant's data
97    int len = DataArrayView::noValues(shape);    int len = getNoValues();
98    m_data.resize(len,0.,len);    m_data.resize(len,0.,len);
99    //    //
100    // create a view of the data with the correct shape    // create a view of the data with the correct shape
101    DataArrayView tempView(m_data,shape);  //   DataArrayView tempView(m_data,shape);
102    DataArrayView::RegionLoopRangeType region_loop_range=getSliceRegionLoopRange(region);    DataTypes::RegionLoopRangeType region_loop_range=DataTypes::getSliceRegionLoopRange(region);
103    //    //
104    // load the view with the data from the slice    // load the view with the data from the slice
105    tempView.copySlice(other.getPointDataView(),region_loop_range);  //   tempView.copySlice(other.getPointDataView(),region_loop_range);
106    setPointDataView(tempView);    DataTypes::copySlice(m_data,getShape(),0,other.getVector(),other.getShape(),0,region_loop_range);
107    //   setPointDataView(tempView);
108  }  }
109    
110  DataConstant::DataConstant(const FunctionSpace& what,  DataConstant::DataConstant(const FunctionSpace& what,
111                             const DataArrayView::ShapeType &shape,                             const DataTypes::ShapeType &shape,
112                             const DataArrayView::ValueType &data)                             const DataTypes::ValueType &data)
113    : DataAbstract(what)    : parent(what,shape)
114  {  {
115    //    //
116    // copy the data in the correct format    // copy the data in the correct format
117    m_data=data;    m_data=data;
118    //    //
119    // create the view of the data    // create the view of the data
120    DataArrayView tempView(m_data,shape);  //   DataArrayView tempView(m_data,shape);
121    setPointDataView(tempView);  //   setPointDataView(tempView);
122  }  }
123    
124  string  string
125  DataConstant::toString() const  DataConstant::toString() const
126  {  {
127    return getPointDataView().toString("");    return DataTypes::pointToString(m_data,getShape(),0,"");
128    }
129    
130    
131    DataAbstract*
132    DataConstant::deepCopy()
133    {
134      return new DataConstant(*this);
135  }  }
136    
137  DataArrayView::ValueType::size_type  
138    DataTypes::ValueType::size_type
139  DataConstant::getPointOffset(int sampleNo,  DataConstant::getPointOffset(int sampleNo,
140                               int dataPointNo) const                               int dataPointNo) const
141  {  {
# Line 113  DataConstant::getPointOffset(int sampleN Line 146  DataConstant::getPointOffset(int sampleN
146    return 0;    return 0;
147  }  }
148    
149  DataArrayView::ValueType::size_type  DataTypes::ValueType::size_type
150  DataConstant::getLength() const  DataConstant::getPointOffset(int sampleNo,
151  {                               int dataPointNo)
   return m_data.size();  
 }  
   
 DataArrayView  
 DataConstant::getDataPoint(int sampleNo,  
                            int dataPointNo)  
152  {  {
153    EsysAssert((validSamplePointNo(dataPointNo) && validSampleNo(sampleNo)),    EsysAssert((validSamplePointNo(dataPointNo) && validSampleNo(sampleNo)),
154               "Invalid index, sampleNo: " << sampleNo << " dataPointNo: " << dataPointNo);                "Invalid index, sampleNo: " << sampleNo << " dataPointNo: " << dataPointNo);
155    //    //
156    // Whatever the coord's always return the same value as this is constant data.    // Whatever the coord's always return the same value as this is constant data.
157    return getPointDataView();    return 0;
158  }  }
159      
160    DataTypes::ValueType::size_type
161    DataConstant::getLength() const
162    {
163      return m_data.size();
164    }
165    
166    // DataArrayView
167    // DataConstant::getDataPoint(int sampleNo,
168    //                            int dataPointNo)
169    // {
170    //   EsysAssert((validSamplePointNo(dataPointNo) && validSampleNo(sampleNo)),
171    //              "Invalid index, sampleNo: " << sampleNo << " dataPointNo: " << dataPointNo);
172    //   //
173    //   // Whatever the coord's always return the same value as this is constant data.
174    //   return getPointDataView();
175    // }
176    
177  DataAbstract*  DataAbstract*
178  DataConstant::getSlice(const DataArrayView::RegionType& region) const  DataConstant::getSlice(const DataTypes::RegionType& region) const
179  {  {
180    return new DataConstant(*this,region);    return new DataConstant(*this,region);
181  }  }
182    
183  void  void
184  DataConstant::setSlice(const DataAbstract* value,  DataConstant::setSlice(const DataAbstract* value,
185                         const DataArrayView::RegionType& region)                         const DataTypes::RegionType& region)
186  {  {
187    const DataConstant* tempDataConst=dynamic_cast<const DataConstant*>(value);    const DataConstant* tempDataConst=dynamic_cast<const DataConstant*>(value);
188    if (tempDataConst==0) {    if (tempDataConst==0) {
189      throw DataException("Programming error - casting to DataConstant.");      throw DataException("Programming error - casting to DataConstant.");
190    }    }
191    //    //
192    DataArrayView::ShapeType shape(DataArrayView::getResultSliceShape(region));    DataTypes::ShapeType shape(DataTypes::getResultSliceShape(region));
193    DataArrayView::RegionLoopRangeType region_loop_range=getSliceRegionLoopRange(region);    DataTypes::RegionLoopRangeType region_loop_range=DataTypes::getSliceRegionLoopRange(region);
194    //    //
195    // check shape:    // check shape:
196    if (getPointDataView().getRank()!=region.size()) {    if (getRank()!=region.size()) {
197      throw DataException("Error - Invalid slice region.");      throw DataException("Error - Invalid slice region.");
198    }    }
199    if (tempDataConst->getPointDataView().getRank()>0 and !value->getPointDataView().checkShape(shape)) {    if (getRank()>0 && !DataTypes::checkShape(value->getShape(),shape)) {
200      throw DataException (value->getPointDataView().createShapeErrorMessage(      throw DataException (DataTypes::createShapeErrorMessage(
201                  "Error - Couldn't copy slice due to shape mismatch.",shape));                  "Error - Couldn't copy slice due to shape mismatch.",shape,value->getShape()));
202    }    }
203    //    //   getPointDataView().copySliceFrom(tempDataConst->getPointDataView(),region_loop_range);
204    getPointDataView().copySliceFrom(tempDataConst->getPointDataView(),region_loop_range);    DataTypes::copySliceFrom(m_data,getShape(),0,tempDataConst->getVector(), tempDataConst->getShape(),0,region_loop_range);
205  }  }
206    
207    
208    
209  void  void
210  DataConstant::reshapeDataPoint(const DataArrayView::ShapeType& shape)  DataConstant::symmetric(DataAbstract* ev)
211  {  {
212    if (getPointDataView().getRank()!=0) {    DataConstant* temp_ev=dynamic_cast<DataConstant*>(ev);
213      stringstream temp;    if (temp_ev==0) {
214      temp << "Error - Can only reshape Data with data points of rank 0. "      throw DataException("Error - DataConstant::symmetric: casting to DataConstant failed (propably a programming error).");
          << "This Data has data points with rank: " << getPointDataView().getRank();  
     throw DataException(temp.str());  
215    }    }
216    int len = DataArrayView::noValues(shape);  /*  DataArrayView& thisView=getPointDataView();
217    m_data.resize(len,getPointDataView()(),len);    DataArrayView& evView=ev->getPointDataView();*/
218    DataArrayView newView(m_data,shape);    DataMaths::symmetric(m_data,getShape(),0,temp_ev->getVector(), temp_ev->getShape(),0);
   setPointDataView(newView);  
219  }  }
220    
221  int  void
222  DataConstant::archiveData(ofstream& archiveFile,  DataConstant::nonsymmetric(DataAbstract* ev)
                           const DataArrayView::ValueType::size_type noValues) const  
223  {  {
224    return(m_data.archiveData(archiveFile, noValues));    DataConstant* temp_ev=dynamic_cast<DataConstant*>(ev);
225      if (temp_ev==0) {
226        throw DataException("Error - DataConstant::nonsymmetric: casting to DataConstant failed (propably a programming error).");
227      }
228    /*  DataArrayView& thisView=getPointDataView();
229      DataArrayView& evView=ev->getPointDataView();*/
230      DataMaths::nonsymmetric(m_data,getShape(),0,temp_ev->getVector(), temp_ev->getShape(),0);
231  }  }
232    
233  int  void
234  DataConstant::extractData(ifstream& archiveFile,  DataConstant::trace(DataAbstract* ev, int axis_offset)
                           const DataArrayView::ValueType::size_type noValues)  
235  {  {
236    return(m_data.extractData(archiveFile, noValues));    DataConstant* temp_ev=dynamic_cast<DataConstant*>(ev);
237      if (temp_ev==0) {
238        throw DataException("Error - DataConstant::trace: casting to DataConstant failed (propably a programming error).");
239      }
240    /*  DataArrayView& thisView=getPointDataView();
241      DataArrayView& evView=ev->getPointDataView();*/
242      ValueType& evVec=temp_ev->getVector();
243      const ShapeType& evShape=temp_ev->getShape();
244      DataMaths::trace(m_data,getShape(),0,evVec,evShape,0,axis_offset);
245    }
246    
247    void
248    DataConstant::swapaxes(DataAbstract* ev, int axis0, int axis1)
249    {
250      DataConstant* temp_ev=dynamic_cast<DataConstant*>(ev);
251      if (temp_ev==0) {
252        throw DataException("Error - DataConstant::swapaxes: casting to DataConstant failed (propably a programming error).");
253      }
254    //   DataArrayView& thisView=getPointDataView();
255    //   DataArrayView& evView=ev->getPointDataView();
256      DataMaths::swapaxes(m_data,getShape(),0,temp_ev->getVector(), temp_ev->getShape(),0,axis0,axis1);
257    }
258    
259    void
260    DataConstant::transpose(DataAbstract* ev, int axis_offset)
261    {
262      DataConstant* temp_ev=dynamic_cast<DataConstant*>(ev);
263      if (temp_ev==0) {
264        throw DataException("Error - DataConstant::transpose: casting to DataConstant failed (propably a programming error).");
265      }
266    /*  DataArrayView& thisView=getPointDataView();
267      DataArrayView& evView=ev->getPointDataView();*/
268      DataMaths::transpose(m_data, getShape(),0, temp_ev->getVector(),temp_ev->getShape(),0,axis_offset);
269  }  }
270    
271  void  void
# Line 196  DataConstant::eigenvalues(DataAbstract* Line 275  DataConstant::eigenvalues(DataAbstract*
275    if (temp_ev==0) {    if (temp_ev==0) {
276      throw DataException("Error - DataConstant::eigenvalues: casting to DataConstant failed (propably a programming error).");      throw DataException("Error - DataConstant::eigenvalues: casting to DataConstant failed (propably a programming error).");
277    }    }
278    DataArrayView& thisView=getPointDataView();  /*  DataArrayView& thisView=getPointDataView();
279    DataArrayView& evView=ev->getPointDataView();    DataArrayView& evView=ev->getPointDataView();*/
280    DataArrayView::eigenvalues(thisView,0,evView,0);    DataMaths::eigenvalues(m_data,getShape(),0,temp_ev->getVector(), temp_ev->getShape(),0);
281  }  }
282  void  void
283  DataConstant::eigenvalues_and_eigenvectors(DataAbstract* ev,DataAbstract* V,const double tol)  DataConstant::eigenvalues_and_eigenvectors(DataAbstract* ev,DataAbstract* V,const double tol)
# Line 211  DataConstant::eigenvalues_and_eigenvecto Line 290  DataConstant::eigenvalues_and_eigenvecto
290    if (temp_V==0) {    if (temp_V==0) {
291      throw DataException("Error - DataConstant::eigenvalues_and_eigenvectors: casting to DataConstant failed (propably a programming error).");      throw DataException("Error - DataConstant::eigenvalues_and_eigenvectors: casting to DataConstant failed (propably a programming error).");
292    }    }
293    DataArrayView thisView=getPointDataView();  //   DataArrayView thisView=getPointDataView();
294    DataArrayView evView=ev->getPointDataView();  //   DataArrayView evView=ev->getPointDataView();
295    DataArrayView VView=V->getPointDataView();  //   DataArrayView VView=V->getPointDataView();
296    
297      DataMaths::eigenvalues_and_eigenvectors(m_data, getShape(),0,temp_ev->getVector(), temp_ev->getShape(),0,temp_V->getVector(), temp_V->getShape(),0,tol);
298    }
299    
300    DataArrayView::eigenvalues_and_eigenvectors(thisView,0,evView,0,VView,tol);  void
301    DataConstant::setToZero()
302    {
303        DataTypes::ValueType::size_type n=m_data.size();
304        for (int i=0; i<n ;++i) m_data[i]=0.;
305  }  }
306    
307    void
308    DataConstant::dump(const std::string fileName) const
309    {
310       #ifdef USE_NETCDF
311       const NcDim* ncdims[DataTypes::maxRank];
312       NcVar* var;
313       int rank = getRank();
314       int type=  getFunctionSpace().getTypeCode();
315       int ndims =0;
316       long dims[DataTypes::maxRank];
317       const double* d_ptr=&(m_data[0]);
318       DataTypes::ShapeType shape = getShape();
319       int mpi_iam=getFunctionSpace().getDomain()->getMPIRank();
320       int mpi_num=getFunctionSpace().getDomain()->getMPISize();
321    #ifdef PASO_MPI
322       MPI_Status status;
323    #endif
324    
325    #ifdef PASO_MPI
326       /* Serialize NetCDF I/O */
327       if (mpi_iam>0) MPI_Recv(&ndims, 0, MPI_INT, mpi_iam-1, 81802, MPI_COMM_WORLD, &status);
328    #endif
329    
330       // netCDF error handler
331       NcError err(NcError::verbose_nonfatal);
332       // Create the file.
333       char *newFileName = Escript_MPI_appendRankToFileName(fileName.c_str(), mpi_num, mpi_iam);
334       NcFile dataFile(newFileName, NcFile::Replace);
335       // check if writing was successful
336       if (!dataFile.is_valid())
337        throw DataException("Error - DataConstant:: opening of netCDF file for output failed.");
338       if (!dataFile.add_att("type_id",0) )
339        throw DataException("Error - DataConstant:: appending data type to netCDF file failed.");
340       if (!dataFile.add_att("rank",rank) )
341        throw DataException("Error - DataConstant:: appending rank attribute to netCDF file failed.");
342       if (!dataFile.add_att("function_space_type",type))
343        throw DataException("Error - DataConstant:: appending function space attribute to netCDF file failed.");
344    
345       if (rank == 0) {
346          if( ! (ncdims[0] = dataFile.add_dim("l", 1)) )
347            throw DataException("Error - DataConstant:: appending ncdimension 0 to netCDF file failed.");
348          dims[0]=1,
349          ndims=1;
350       } else {
351           ndims=rank;
352           dims[0]=shape[0];
353           if (! (ncdims[0] = dataFile.add_dim("d0",shape[0])) )
354            throw DataException("Error - DataConstant:: appending ncdimension 0 to netCDF file failed.");
355           if ( rank >1 ) {
356               dims[1]=shape[1];
357               if (! (ncdims[1] = dataFile.add_dim("d1",shape[1])) )
358            throw DataException("Error - DataConstant:: appending ncdimension 1 to netCDF file failed.");
359           }
360           if ( rank >2 ) {
361               dims[2]=shape[2];
362               if (! (ncdims[2] = dataFile.add_dim("d2", shape[2])) )
363            throw DataException("Error - DataConstant:: appending ncdimension 2 to netCDF file failed.");
364           }
365           if ( rank >3 ) {
366               dims[3]=shape[3];
367               if (! (ncdims[3] = dataFile.add_dim("d3", shape[3])) )
368            throw DataException("Error - DataConstant:: appending ncdimension 3 to netCDF file failed.");
369           }
370       }
371    
372       if (! ( var = dataFile.add_var("data", ncDouble, ndims, ncdims)) )
373        throw DataException("Error - DataConstant:: appending variable to netCDF file failed.");
374       if (! (var->put(d_ptr,dims)) )
375             throw DataException("Error - DataConstant:: copy data to netCDF buffer failed.");
376    #ifdef PASO_MPI
377       if (mpi_iam<mpi_num-1) MPI_Send(&ndims, 0, MPI_INT, mpi_iam+1, 81802, MPI_COMM_WORLD);
378    #endif
379       #else
380       throw DataException("Error - DataConstant:: dump is not configured with netCDF. Please contact your installation manager.");
381       #endif
382    }
383    
384  }  // end of namespace  }  // end of namespace

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