/[escript]/trunk/escript/src/DataExpanded.cpp
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trunk/esys2/escript/src/Data/DataExpanded.cpp revision 102 by jgs, Wed Dec 15 07:08:39 2004 UTC temp_trunk_copy/escript/src/DataExpanded.cpp revision 1384 by phornby, Fri Jan 11 02:29:38 2008 UTC
# Line 1  Line 1 
 // $Id$  
 /*  
  ******************************************************************************  
  *                                                                            *  
  *       COPYRIGHT  ACcESS 2004 -  All Rights Reserved                        *  
  *                                                                            *  
  * This software is the property of ACcESS. No part of this code              *  
  * may be copied in any form or by any means without the expressed written    *  
  * consent of ACcESS.  Copying, use or modification of this software          *  
  * by any unauthorised person is illegal unless that person has a software    *  
  * license agreement with ACcESS.                                             *  
  *                                                                            *  
  ******************************************************************************  
 */  
   
 #include "escript/Data/DataException.h"  
 #include "escript/Data/DataExpanded.h"  
 #include "escript/Data/DataConstant.h"  
 #include "escript/Data/DataTagged.h"  
 #include "escript/Data/DataArrayView.h"  
1    
2  #include <boost/python/extract.hpp>  /* $Id$ */
3    
4    /*******************************************************
5     *
6     *           Copyright 2003-2007 by ACceSS MNRF
7     *       Copyright 2007 by University of Queensland
8     *
9     *                http://esscc.uq.edu.au
10     *        Primary Business: Queensland, Australia
11     *  Licensed under the Open Software License version 3.0
12     *     http://www.opensource.org/licenses/osl-3.0.php
13     *
14     *******************************************************/
15    
16    #include "DataExpanded.h"
17    #include "DataException.h"
18    #include "DataConstant.h"
19    #include "DataTagged.h"
20    #ifdef USE_NETCDF
21    #include <netcdfcpp.h>
22    #endif
23    
24  #include <iostream>  #include <boost/python/extract.hpp>
25    
26  using namespace std;  using namespace std;
27  using namespace boost::python;  using namespace boost::python;
# Line 35  DataExpanded::DataExpanded(const boost:: Line 35  DataExpanded::DataExpanded(const boost::
35  {  {
36    DataArrayView::ShapeType tempShape;    DataArrayView::ShapeType tempShape;
37    //    //
38    // extract the shape from the python array    // extract the shape of the python numarray
39    for (int i=0; i<value.getrank(); ++i) {    for (int i=0; i<value.getrank(); i++) {
     //cout << extract<int>(value.getshape()[i]) << endl;  
40      tempShape.push_back(extract<int>(value.getshape()[i]));      tempShape.push_back(extract<int>(value.getshape()[i]));
41    }    }
42      //
43      // initialise the data array for this object
44    initialise(tempShape,what.getNumSamples(),what.getNumDPPSample());    initialise(tempShape,what.getNumSamples(),what.getNumDPPSample());
45    //    //
46    // copy the given value to every data point    // copy the given value to every data point
# Line 49  DataExpanded::DataExpanded(const boost:: Line 50  DataExpanded::DataExpanded(const boost::
50  DataExpanded::DataExpanded(const DataExpanded& other)  DataExpanded::DataExpanded(const DataExpanded& other)
51    : DataAbstract(other.getFunctionSpace()),    : DataAbstract(other.getFunctionSpace()),
52    m_data(other.m_data)    m_data(other.m_data)
53  {      {
54    //    //
55    // create the view for the data    // create the view for the data
56    DataArrayView temp(m_data.getData(),other.getPointDataView().getShape());    DataArrayView temp(m_data.getData(),other.getPointDataView().getShape());
# Line 58  DataExpanded::DataExpanded(const DataExp Line 59  DataExpanded::DataExpanded(const DataExp
59    
60  DataExpanded::DataExpanded(const DataConstant& other)  DataExpanded::DataExpanded(const DataConstant& other)
61    : DataAbstract(other.getFunctionSpace())    : DataAbstract(other.getFunctionSpace())
62  {      {
63      //
64      // initialise the data array for this object
65    initialise(other.getPointDataView().getShape(),other.getNumSamples(),other.getNumDPPSample());    initialise(other.getPointDataView().getShape(),other.getNumSamples(),other.getNumDPPSample());
66    //    //
67    // DataConstant only has one value    // DataConstant only has one value, copy this to every data point
68    copy(other.getPointDataView());    copy(other.getPointDataView());
69  }  }
70    
71  DataExpanded::DataExpanded(const DataTagged& other)  DataExpanded::DataExpanded(const DataTagged& other)
72    : DataAbstract(other.getFunctionSpace())    : DataAbstract(other.getFunctionSpace())
73  {      {
74      //
75      // initialise the data array for this object
76    initialise(other.getPointDataView().getShape(),other.getNumSamples(),other.getNumDPPSample());    initialise(other.getPointDataView().getShape(),other.getNumSamples(),other.getNumDPPSample());
77      //
78      // for each data point in this object, extract and copy the corresponding data
79      // value from the given DataTagged object
80    int i,j;    int i,j;
81    DataArrayView::ValueType::size_type numRows=m_data.getNumRows();    DataArrayView::ValueType::size_type numRows=m_data.getNumRows();
82    DataArrayView::ValueType::size_type numCols=m_data.getNumCols();    DataArrayView::ValueType::size_type numCols=m_data.getNumCols();
83  #pragma omp parallel for private(i,j) schedule(static)    #pragma omp parallel for private(i,j) schedule(static)
84    for (i=0;i<numRows;++i) {    for (i=0;i<numRows;i++) {
85      for (j=0;j<numCols;++j) {      for (j=0;j<numCols;j++) {
86        try {        try {
87          getPointDataView().copy(getPointOffset(i,j), other.getPointDataView(), other.getPointOffset(i,j));          getPointDataView().copy(getPointOffset(i,j),
88                                    other.getPointDataView(),
89                                    other.getPointOffset(i,j));
90        }        }
91        catch (std::exception& e) {        catch (std::exception& e) {
92          cout << e.what() << endl;          cout << e.what() << endl;
# Line 97  DataExpanded::DataExpanded(const DataExp Line 107  DataExpanded::DataExpanded(const DataExp
107    initialise(shape,other.getNumSamples(),other.getNumDPPSample());    initialise(shape,other.getNumSamples(),other.getNumDPPSample());
108    //    //
109    // copy the data    // copy the data
110      DataArrayView::RegionLoopRangeType region_loop_range=getSliceRegionLoopRange(region);
111    DataArrayView::ValueType::size_type numRows=m_data.getNumRows();    DataArrayView::ValueType::size_type numRows=m_data.getNumRows();
112    DataArrayView::ValueType::size_type numCols=m_data.getNumCols();    DataArrayView::ValueType::size_type numCols=m_data.getNumCols();
113    int i,j;    int i,j;
114  #pragma omp parallel for private(i,j) schedule(static)    #pragma omp parallel for private(i,j) schedule(static)
115    for (i=0;i<numRows;++i) {    for (i=0;i<numRows;i++) {
116      for (j=0;j<numCols;++j) {      for (j=0;j<numCols;j++) {
117        try {        try {
118          getPointDataView().copySlice(getPointOffset(i,j),other.getPointDataView(),other.getPointOffset(i,j),region);          getPointDataView().copySlice(getPointOffset(i,j),
119                                         other.getPointDataView(),
120                                         other.getPointOffset(i,j),
121                                         region_loop_range);
122        }        }
123        catch (std::exception& e) {        catch (std::exception& e) {
124          cout << e.what() << endl;          cout << e.what() << endl;
# Line 117  DataExpanded::DataExpanded(const DataArr Line 131  DataExpanded::DataExpanded(const DataArr
131                             const FunctionSpace& what)                             const FunctionSpace& what)
132    : DataAbstract(what)    : DataAbstract(what)
133  {  {
134      //
135      // get the shape of the given data value
136    DataArrayView::ShapeType tempShape=value.getShape();    DataArrayView::ShapeType tempShape=value.getShape();
137      //
138      // initialise this Data object to the shape of the given data value
139    initialise(tempShape,what.getNumSamples(),what.getNumDPPSample());    initialise(tempShape,what.getNumSamples(),what.getNumDPPSample());
140      //
141      // copy the given value to every data point
142    copy(value);    copy(value);
143  }  }
144    
145  DataExpanded::~DataExpanded()  DataExpanded::DataExpanded(const FunctionSpace& what,
146                               const DataArrayView::ShapeType &shape,
147                               const DataArrayView::ValueType &data)
148      : DataAbstract(what)
149  {  {
150      //
151      // create the view of the data
152      initialise(shape,what.getNumSamples(),what.getNumDPPSample());
153      //
154      // copy the data in the correct format
155      m_data.getData()=data;
156  }  }
157    
158  void  DataExpanded::~DataExpanded()
 DataExpanded::reshapeDataPoint(const DataArrayView::ShapeType& shape)  
159  {  {
   //  
   // reshape a rank zero data point  
   if (getPointDataView().getRank()!=0) {  
     stringstream temp;  
     temp << "Error - Can only reshape Data with data points of rank 0. "  
          << "This Data has data points with rank: "  
          << getPointDataView().getRank();  
     throw DataException(temp.str());  
   }  
   DataBlocks2D newData(getNumSamples(),getNumDPPSample(), DataArrayView::noValues(shape));  
   DataArrayView newView(newData.getData(),shape);  
   //  
   // Copy the original data to every value for the new shape  
   int i,j;  
   int nRows=m_data.getNumRows();  
   int nCols=m_data.getNumCols();  
 #pragma omp parallel for private(i,j) schedule(static)  
   for (i=0;i<nRows;++i) {  
     for (j=0;j<nCols;++j) {  
       //  
       // Copy the data into the specified offset  
       // NOTE: An exception may be thown from this call if  
       // DOASSERT is on which of course will play  
       // havoc with the omp threads. Run single threaded  
       // if using DOASSERT.  
       newView.copy(newData.index(i,j),m_data.getData()[m_data.index(i,j)]);  
     }  
   }  
   m_data.Swap(newData);  
   DataArrayView temp(m_data.getData(),shape);  
   setPointDataView(temp);  
160  }  }
161    
162  DataAbstract*  DataAbstract*
163  DataExpanded::getSlice(const DataArrayView::RegionType& region) const  DataExpanded::getSlice(const DataArrayView::RegionType& region) const
164  {  {
165    return new DataExpanded(*this,region);    return new DataExpanded(*this,region);
166  }  }
167    
168  void  void
169  DataExpanded::setSlice(const DataAbstract* value,  DataExpanded::setSlice(const DataAbstract* value,
170                         const DataArrayView::RegionType& region)                         const DataArrayView::RegionType& region)
171  {  {
172    const DataExpanded* tempDataExp=dynamic_cast<const DataExpanded*>(value);    const DataExpanded* tempDataExp=dynamic_cast<const DataExpanded*>(value);
173    if (tempDataExp==0) {    if (tempDataExp==0) {
174      throw DataException("Programming error - casting to DataExpanded.");      throw DataException("Programming error - casting to DataExpanded.");
175    }    }
176      //
177      // get shape of slice
178      DataArrayView::ShapeType shape(DataArrayView::getResultSliceShape(region));
179      DataArrayView::RegionLoopRangeType region_loop_range=getSliceRegionLoopRange(region);
180      //
181      // check shape
182    if (getPointDataView().getRank()!=region.size()) {    if (getPointDataView().getRank()!=region.size()) {
183      throw DataException("Error - Invalid slice region.");      throw DataException("Error - Invalid slice region.");
184    }    }
185    if (!value->getPointDataView().checkShape(DataArrayView::getResultSliceShape(region))) {    if (tempDataExp->getPointDataView().getRank()>0 && !value->getPointDataView().checkShape(shape)) {
186      throw DataException (value->getPointDataView().createShapeErrorMessage(      throw DataException (value->getPointDataView().createShapeErrorMessage(
187          "Error - Couldn't copy slice due to shape mismatch.",DataArrayView::getResultSliceShape(region)));          "Error - Couldn't copy slice due to shape mismatch.",shape));
188    }    }
189    //    //
190    // copy the data    // copy the data from the slice into this object
191    DataArrayView::ValueType::size_type numRows=m_data.getNumRows();    DataArrayView::ValueType::size_type numRows=m_data.getNumRows();
192    DataArrayView::ValueType::size_type numCols=m_data.getNumCols();    DataArrayView::ValueType::size_type numCols=m_data.getNumCols();
193    int i, j;    int i, j;
194  #pragma omp parallel for private(i,j) schedule(static)    #pragma omp parallel for private(i,j) schedule(static)
195    for (i=0;i<numRows;i++) {    for (i=0;i<numRows;i++) {
196      for (j=0;j<numCols;j++) {      for (j=0;j<numCols;j++) {
197        getPointDataView().copySliceFrom(getPointOffset(i,j),tempDataExp->getPointDataView(),tempDataExp->getPointOffset(i,j),region);        getPointDataView().copySliceFrom(getPointOffset(i,j),
198                                           tempDataExp->getPointDataView(),
199                                           tempDataExp->getPointOffset(i,j),
200                                           region_loop_range);
201      }      }
202    }    }
203  }  }
204    
205  void  void
206  DataExpanded::copy(const DataArrayView& value)  DataExpanded::copy(const DataArrayView& value)
207  {  {
208    //    //
209    // Copy a single value to every data point    // copy a single value to every data point in this object
210    int nRows=m_data.getNumRows();    int nRows=m_data.getNumRows();
211    int nCols=m_data.getNumCols();    int nCols=m_data.getNumCols();
212    int i, j;    int i,j;
213  #pragma omp parallel for private(i,j) schedule(static)    #pragma omp parallel for private(i,j) schedule(static)
214    for (i=0;i<nRows;++i) {    for (i=0;i<nRows;i++) {
215      for (j=0;j<nCols;++j) {      for (j=0;j<nCols;j++) {
216        //        // NOTE: An exception may be thown from this call if
       // Copy the data into the specified offset  
       // NOTE: An exception may be thown from this call if  
217        // DOASSERT is on which of course will play        // DOASSERT is on which of course will play
218        // havoc with the omp threads. Run single threaded        // havoc with the omp threads. Run single threaded
219        // if using DOASSERT.        // if using DOASSERT.
220        getPointDataView().copy(m_data.index(i,j),value);        getPointDataView().copy(getPointOffset(i,j),value);
221      }      }
222    }    }
223  }  }
224    
225  void  void
226  DataExpanded::copy(const boost::python::numeric::array& value)  DataExpanded::copy(const boost::python::numeric::array& value)
227  {  {
228    
229      // extract the shape of the numarray
230      DataArrayView::ShapeType tempShape;
231      for (int i=0; i < value.getrank(); i++) {
232        tempShape.push_back(extract<int>(value.getshape()[i]));
233      }
234    
235      // get the space for the data vector
236      int len = DataArrayView::noValues(tempShape);
237      DataVector temp_data(len, 0.0, len);
238      DataArrayView temp_dataView(temp_data, tempShape);
239      temp_dataView.copy(value);
240    
241    //    //
242    // first convert the numarray into a DataArrayView format    // check the input shape matches this shape
243    DataArray temp(value);    if (!getPointDataView().checkShape(temp_dataView.getShape())) {
   //  
   // check the input shape matches this shape, this will throw an exception  
   if (!getPointDataView().checkShape(temp.getView().getShape())) {  
244      throw DataException(getPointDataView().createShapeErrorMessage(      throw DataException(getPointDataView().createShapeErrorMessage(
245                          "Error - (DataExpanded) Cannot copy due to shape mismatch.",                          "Error - (DataExpanded) Cannot copy due to shape mismatch.",
246                          temp.getView().getShape()));                          temp_dataView.getShape()));
247    }    }
248    //    //
249    // now copy over the entire data structure    // now copy over the data
250    copy(temp.getView());    copy(temp_dataView);
251  }  }
252    
253  void  void
# Line 242  DataExpanded::initialise(const DataArray Line 256  DataExpanded::initialise(const DataArray
256                           int noDataPointsPerSample)                           int noDataPointsPerSample)
257  {  {
258    //    //
259    // resize data to the required size    // resize data array to the required size
260    m_data.resize(noSamples,noDataPointsPerSample,DataArrayView::noValues(shape));    m_data.resize(noSamples,noDataPointsPerSample,DataArrayView::noValues(shape));
261    //    //
262    // create a point data viewer of the data    // create the data view of the data array
263    DataArrayView temp(m_data.getData(),shape);    DataArrayView temp(m_data.getData(),shape);
264    setPointDataView(temp);    setPointDataView(temp);
265  }  }
# Line 254  string Line 268  string
268  DataExpanded::toString() const  DataExpanded::toString() const
269  {  {
270    stringstream temp;    stringstream temp;
271      FunctionSpace fs=getFunctionSpace();
272    //    //
273    // create a temporary view as the offset will be changed    // create a temporary view as the offset will be changed
274    DataArrayView tempView(getPointDataView().getData(),getPointDataView().getShape(),getPointDataView().getOffset());    DataArrayView tempView(getPointDataView().getData(),getPointDataView().getShape(),getPointDataView().getOffset());
275    for (int i=0;i<m_data.getNumRows();++i) {    for (int i=0;i<m_data.getNumRows();i++) {
276      for (int j=0;j<m_data.getNumCols();++j) {      for (int j=0;j<m_data.getNumCols();j++) {
277        tempView.setOffset(m_data.index(i,j));        tempView.setOffset(getPointOffset(i,j));
278        stringstream suffix;        stringstream suffix;
279        suffix << "(" << i << "," << j << ")";        suffix << "( id: " << i << ", ref: " << fs.getReferenceIDOfSample(i) << ", pnt: " << j << ")";
280        temp << tempView.toString(suffix.str());        temp << tempView.toString(suffix.str());
281        if (!(i==(m_data.getNumRows()-1) && j==(m_data.getNumCols()-1))) {        if (!(i==(m_data.getNumRows()-1) && j==(m_data.getNumCols()-1))) {
282          temp << endl;          temp << endl;
# Line 282  DataArrayView Line 297  DataArrayView
297  DataExpanded::getDataPoint(int sampleNo,  DataExpanded::getDataPoint(int sampleNo,
298                             int dataPointNo)                             int dataPointNo)
299  {  {
300    DataArrayView temp(m_data.getData(),getPointDataView().getShape(),m_data.index(sampleNo,dataPointNo));    DataArrayView temp(m_data.getData(),getPointDataView().getShape(),getPointOffset(sampleNo,dataPointNo));
301    return temp;    return temp;
302  }  }
303    
304  DataArrayView::ValueType::size_type  DataArrayView::ValueType::size_type
305  DataExpanded::getLength() const  DataExpanded::getLength() const
306  {  {
307    return m_data.getData().size();    return m_data.size();
308    }
309    
310    int
311    DataExpanded::archiveData(ofstream& archiveFile,
312                              const DataArrayView::ValueType::size_type noValues) const
313    {
314      return(m_data.archiveData(archiveFile, noValues));
315    }
316    
317    int
318    DataExpanded::extractData(ifstream& archiveFile,
319                              const DataArrayView::ValueType::size_type noValues)
320    {
321      return(m_data.extractData(archiveFile, noValues));
322    }
323    
324    void
325    DataExpanded::copyToDataPoint(const int sampleNo, const int dataPointNo, const double value) {
326      //
327      // Get the number of samples and data-points per sample.
328      int numSamples = getNumSamples();
329      int numDataPointsPerSample = getNumDPPSample();
330      int dataPointRank = getPointDataView().getRank();
331      ShapeType dataPointShape = getPointDataView().getShape();
332      if (numSamples*numDataPointsPerSample > 0) {
333         //TODO: global error handling
334         if ((sampleNo >= numSamples) || (sampleNo < 0 )) {
335              throw DataException("Error - DataExpanded::copyDataPoint invalid sampleNo.");
336         }
337         if ((dataPointNo >= numDataPointsPerSample) || (dataPointNo < 0)) {
338               throw DataException("Error - DataExpanded::copyDataPoint invalid dataPointNoInSample.");
339         }
340         DataArrayView dataPointView = getDataPoint(sampleNo, dataPointNo);
341         if (dataPointRank==0) {
342             dataPointView()=value;
343         } else if (dataPointRank==1) {
344            for (int i=0; i<dataPointShape[0]; i++) {
345                dataPointView(i)=value;
346            }
347         } else if (dataPointRank==2) {
348            for (int i=0; i<dataPointShape[0]; i++) {
349               for (int j=0; j<dataPointShape[1]; j++) {
350                  dataPointView(i,j)=value;
351               }
352            }
353         } else if (dataPointRank==3) {
354            for (int i=0; i<dataPointShape[0]; i++) {
355               for (int j=0; j<dataPointShape[1]; j++) {
356                  for (int k=0; k<dataPointShape[2]; k++) {
357                     dataPointView(i,j,k)=value;
358                  }
359               }
360            }
361         } else if (dataPointRank==4) {
362             for (int i=0; i<dataPointShape[0]; i++) {
363               for (int j=0; j<dataPointShape[1]; j++) {
364                 for (int k=0; k<dataPointShape[2]; k++) {
365                   for (int l=0; l<dataPointShape[3]; l++) {
366                      dataPointView(i,j,k,l)=value;
367                   }
368                 }
369               }
370             }
371         }
372      }
373    }
374    void
375    DataExpanded::copyToDataPoint(const int sampleNo, const int dataPointNo, const boost::python::numeric::array& value) {
376      //
377      // Get the number of samples and data-points per sample.
378      int numSamples = getNumSamples();
379      int numDataPointsPerSample = getNumDPPSample();
380      int dataPointRank = getPointDataView().getRank();
381      ShapeType dataPointShape = getPointDataView().getShape();
382      //
383      // check rank:
384      if (value.getrank()!=dataPointRank)
385           throw DataException("Rank of numarray does not match Data object rank");
386      if (numSamples*numDataPointsPerSample > 0) {
387         //TODO: global error handling
388         if ((sampleNo >= numSamples) || (sampleNo < 0 )) {
389              throw DataException("Error - DataExpanded::copyDataPoint invalid sampleNo.");
390         }
391         if ((dataPointNo >= numDataPointsPerSample) || (dataPointNo < 0)) {
392               throw DataException("Error - DataExpanded::copyDataPoint invalid dataPointNoInSample.");
393         }
394         DataArrayView dataPointView = getDataPoint(sampleNo, dataPointNo);
395         if (dataPointRank==0) {
396             dataPointView()=extract<double>(value[0]);
397         } else if (dataPointRank==1) {
398            for (int i=0; i<dataPointShape[0]; i++) {
399                dataPointView(i)=extract<double>(value[i]);
400            }
401         } else if (dataPointRank==2) {
402            for (int i=0; i<dataPointShape[0]; i++) {
403               for (int j=0; j<dataPointShape[1]; j++) {
404                  dataPointView(i,j)=extract<double>(value[i][j]);
405               }
406            }
407         } else if (dataPointRank==3) {
408            for (int i=0; i<dataPointShape[0]; i++) {
409               for (int j=0; j<dataPointShape[1]; j++) {
410                  for (int k=0; k<dataPointShape[2]; k++) {
411                     dataPointView(i,j,k)=extract<double>(value[i][j][k]);
412                  }
413               }
414            }
415         } else if (dataPointRank==4) {
416             for (int i=0; i<dataPointShape[0]; i++) {
417               for (int j=0; j<dataPointShape[1]; j++) {
418                 for (int k=0; k<dataPointShape[2]; k++) {
419                   for (int l=0; l<dataPointShape[3]; l++) {
420                      dataPointView(i,j,k,l)=extract<double>(value[i][j][k][l]);
421                   }
422                 }
423               }
424             }
425         }
426      }
427    }
428    void
429    DataExpanded::copyAll(const boost::python::numeric::array& value) {
430      //
431      // Get the number of samples and data-points per sample.
432      int numSamples = getNumSamples();
433      int numDataPointsPerSample = getNumDPPSample();
434      int dataPointRank = getPointDataView().getRank();
435      ShapeType dataPointShape = getPointDataView().getShape();
436      //
437      // check rank:
438      if (value.getrank()!=dataPointRank+1)
439           throw DataException("Rank of numarray does not match Data object rank");
440      if (value.getshape()[0]!=numSamples*numDataPointsPerSample)
441           throw DataException("leading dimension of numarray is too small");
442      //
443      int dataPoint = 0;
444      for (int sampleNo = 0; sampleNo < numSamples; sampleNo++) {
445        for (int dataPointNo = 0; dataPointNo < numDataPointsPerSample; dataPointNo++) {
446          DataArrayView dataPointView = getDataPoint(sampleNo, dataPointNo);
447          if (dataPointRank==0) {
448             dataPointView()=extract<double>(value[dataPoint]);
449          } else if (dataPointRank==1) {
450             for (int i=0; i<dataPointShape[0]; i++) {
451                dataPointView(i)=extract<double>(value[dataPoint][i]);
452             }
453          } else if (dataPointRank==2) {
454             for (int i=0; i<dataPointShape[0]; i++) {
455               for (int j=0; j<dataPointShape[1]; j++) {
456                 dataPointView(i,j)=extract<double>(value[dataPoint][i][j]);
457               }
458             }
459           } else if (dataPointRank==3) {
460             for (int i=0; i<dataPointShape[0]; i++) {
461               for (int j=0; j<dataPointShape[1]; j++) {
462                 for (int k=0; k<dataPointShape[2]; k++) {
463                     dataPointView(i,j,k)=extract<double>(value[dataPoint][i][j][k]);
464                 }
465               }
466             }
467           } else if (dataPointRank==4) {
468             for (int i=0; i<dataPointShape[0]; i++) {
469               for (int j=0; j<dataPointShape[1]; j++) {
470                 for (int k=0; k<dataPointShape[2]; k++) {
471                   for (int l=0; l<dataPointShape[3]; l++) {
472                     dataPointView(i,j,k,l)=extract<double>(value[dataPoint][i][j][k][l]);
473                   }
474                 }
475               }
476             }
477          }
478          dataPoint++;
479        }
480      }
481    }
482    void
483    DataExpanded::symmetric(DataAbstract* ev)
484    {
485      int sampleNo,dataPointNo;
486      int numSamples = getNumSamples();
487      int numDataPointsPerSample = getNumDPPSample();
488      DataExpanded* temp_ev=dynamic_cast<DataExpanded*>(ev);
489      if (temp_ev==0) {
490        throw DataException("Error - DataExpanded::symmetric: casting to DataExpanded failed (propably a programming error).");
491      }
492      DataArrayView& thisView=getPointDataView();
493      DataArrayView& evView=ev->getPointDataView();
494      #pragma omp parallel for private(sampleNo,dataPointNo) schedule(static)
495      for (sampleNo = 0; sampleNo < numSamples; sampleNo++) {
496        for (dataPointNo = 0; dataPointNo < numDataPointsPerSample; dataPointNo++) {
497             DataArrayView::symmetric(thisView,getPointOffset(sampleNo,dataPointNo),
498                                        evView,ev->getPointOffset(sampleNo,dataPointNo));
499        }
500      }
501    }
502    void
503    DataExpanded::nonsymmetric(DataAbstract* ev)
504    {
505      int sampleNo,dataPointNo;
506      int numSamples = getNumSamples();
507      int numDataPointsPerSample = getNumDPPSample();
508      DataExpanded* temp_ev=dynamic_cast<DataExpanded*>(ev);
509      if (temp_ev==0) {
510        throw DataException("Error - DataExpanded::nonsymmetric: casting to DataExpanded failed (propably a programming error).");
511      }
512      DataArrayView& thisView=getPointDataView();
513      DataArrayView& evView=ev->getPointDataView();
514      #pragma omp parallel for private(sampleNo,dataPointNo) schedule(static)
515      for (sampleNo = 0; sampleNo < numSamples; sampleNo++) {
516        for (dataPointNo = 0; dataPointNo < numDataPointsPerSample; dataPointNo++) {
517             DataArrayView::nonsymmetric(thisView,getPointOffset(sampleNo,dataPointNo),
518                                        evView,ev->getPointOffset(sampleNo,dataPointNo));
519        }
520      }
521    }
522    void
523    DataExpanded::trace(DataAbstract* ev, int axis_offset)
524    {
525      int sampleNo,dataPointNo;
526      int numSamples = getNumSamples();
527      int numDataPointsPerSample = getNumDPPSample();
528      DataExpanded* temp_ev=dynamic_cast<DataExpanded*>(ev);
529      if (temp_ev==0) {
530        throw DataException("Error - DataExpanded::trace: casting to DataExpanded failed (propably a programming error).");
531      }
532      DataArrayView& thisView=getPointDataView();
533      DataArrayView& evView=ev->getPointDataView();
534      #pragma omp parallel for private(sampleNo,dataPointNo) schedule(static)
535      for (sampleNo = 0; sampleNo < numSamples; sampleNo++) {
536        for (dataPointNo = 0; dataPointNo < numDataPointsPerSample; dataPointNo++) {
537             DataArrayView::trace(thisView,getPointOffset(sampleNo,dataPointNo),
538                                        evView,ev->getPointOffset(sampleNo,dataPointNo),axis_offset);
539        }
540      }
541    }
542    
543    void
544    DataExpanded::transpose(DataAbstract* ev, int axis_offset)
545    {
546      int sampleNo,dataPointNo;
547      int numSamples = getNumSamples();
548      int numDataPointsPerSample = getNumDPPSample();
549      DataExpanded* temp_ev=dynamic_cast<DataExpanded*>(ev);
550      if (temp_ev==0) {
551        throw DataException("Error - DataExpanded::transpose: casting to DataExpanded failed (propably a programming error).");
552      }
553      DataArrayView& thisView=getPointDataView();
554      DataArrayView& evView=ev->getPointDataView();
555      #pragma omp parallel for private(sampleNo,dataPointNo) schedule(static)
556      for (sampleNo = 0; sampleNo < numSamples; sampleNo++) {
557        for (dataPointNo = 0; dataPointNo < numDataPointsPerSample; dataPointNo++) {
558             DataArrayView::transpose(thisView,getPointOffset(sampleNo,dataPointNo),
559                                        evView,ev->getPointOffset(sampleNo,dataPointNo),axis_offset);
560        }
561      }
562    }
563    
564    void
565    DataExpanded::swapaxes(DataAbstract* ev, int axis0, int axis1)
566    {
567      int sampleNo,dataPointNo;
568      int numSamples = getNumSamples();
569      int numDataPointsPerSample = getNumDPPSample();
570      DataExpanded* temp_ev=dynamic_cast<DataExpanded*>(ev);
571      if (temp_ev==0) {
572        throw DataException("Error - DataExpanded::swapaxes: casting to DataExpanded failed (propably a programming error).");
573      }
574      DataArrayView& thisView=getPointDataView();
575      DataArrayView& evView=ev->getPointDataView();
576      #pragma omp parallel for private(sampleNo,dataPointNo) schedule(static)
577      for (sampleNo = 0; sampleNo < numSamples; sampleNo++) {
578        for (dataPointNo = 0; dataPointNo < numDataPointsPerSample; dataPointNo++) {
579             DataArrayView::swapaxes(thisView,getPointOffset(sampleNo,dataPointNo),
580                                        evView,ev->getPointOffset(sampleNo,dataPointNo),axis0,axis1);
581        }
582      }
583    }
584    void
585    DataExpanded::eigenvalues(DataAbstract* ev)
586    {
587      int sampleNo,dataPointNo;
588      int numSamples = getNumSamples();
589      int numDataPointsPerSample = getNumDPPSample();
590      DataExpanded* temp_ev=dynamic_cast<DataExpanded*>(ev);
591      if (temp_ev==0) {
592        throw DataException("Error - DataExpanded::eigenvalues: casting to DataExpanded failed (propably a programming error).");
593      }
594      DataArrayView& thisView=getPointDataView();
595      DataArrayView& evView=ev->getPointDataView();
596      #pragma omp parallel for private(sampleNo,dataPointNo) schedule(static)
597      for (sampleNo = 0; sampleNo < numSamples; sampleNo++) {
598        for (dataPointNo = 0; dataPointNo < numDataPointsPerSample; dataPointNo++) {
599             DataArrayView::eigenvalues(thisView,getPointOffset(sampleNo,dataPointNo),
600                                        evView,ev->getPointOffset(sampleNo,dataPointNo));
601        }
602      }
603    }
604    void
605    DataExpanded::eigenvalues_and_eigenvectors(DataAbstract* ev,DataAbstract* V,const double tol)
606    {
607      int numSamples = getNumSamples();
608      int numDataPointsPerSample = getNumDPPSample();
609      int sampleNo,dataPointNo;
610      DataExpanded* temp_ev=dynamic_cast<DataExpanded*>(ev);
611      if (temp_ev==0) {
612        throw DataException("Error - DataExpanded::eigenvalues_and_eigenvectors: casting to DataExpanded failed (propably a programming error).");
613      }
614      DataExpanded* temp_V=dynamic_cast<DataExpanded*>(V);
615      if (temp_V==0) {
616        throw DataException("Error - DataExpanded::eigenvalues_and_eigenvectors: casting to DataExpanded failed (propably a programming error).");
617      }
618      DataArrayView& thisView=getPointDataView();
619      DataArrayView& evView=ev->getPointDataView();
620      DataArrayView& VView=V->getPointDataView();
621      #pragma omp parallel for private(sampleNo,dataPointNo) schedule(static)
622      for (sampleNo = 0; sampleNo < numSamples; sampleNo++) {
623        for (dataPointNo = 0; dataPointNo < numDataPointsPerSample; dataPointNo++) {
624             DataArrayView::eigenvalues_and_eigenvectors(thisView,getPointOffset(sampleNo,dataPointNo),
625                                                         evView,ev->getPointOffset(sampleNo,dataPointNo),
626                                                         VView,V->getPointOffset(sampleNo,dataPointNo),
627                                                         tol);
628        }
629      }
630  }  }
631    
632    void
633    DataExpanded::setToZero(){
634      int numSamples = getNumSamples();
635      int numDataPointsPerSample = getNumDPPSample();
636      DataArrayView& thisView=getPointDataView();
637      DataArrayView::ValueType::size_type n = thisView.noValues();
638      double* p;
639      int  sampleNo,dataPointNo, i;
640      #pragma omp parallel for private(sampleNo,dataPointNo,p,i) schedule(static)
641      for (sampleNo = 0; sampleNo < numSamples; sampleNo++) {
642        for (dataPointNo = 0; dataPointNo < numDataPointsPerSample; dataPointNo++) {
643            p=&(m_data[getPointOffset(sampleNo,dataPointNo)]);
644            for (int i=0; i<n ;++i) p[i]=0.;
645        }
646      }
647    }
648    
649    
650    void
651    DataExpanded::dump(const std::string fileName) const
652    {
653       #ifdef PASO_MPI
654       throw DataException("Error - DataExpanded:: dump is not implemented for MPI yet.");
655       #endif
656       #ifdef USE_NETCDF
657       const int ldims=2+DataArrayView::maxRank;
658       const NcDim* ncdims[ldims];
659       NcVar *var, *ids;
660       int rank = getPointDataView().getRank();
661       int type=  getFunctionSpace().getTypeCode();
662       int ndims =0;
663       long dims[ldims];
664       const double* d_ptr=&(m_data[0]);
665       DataArrayView::ShapeType shape = getPointDataView().getShape();
666    
667       // netCDF error handler
668       NcError err(NcError::verbose_nonfatal);
669       // Create the file.
670       NcFile dataFile(fileName.c_str(), NcFile::Replace);
671       // check if writing was successful
672       if (!dataFile.is_valid())
673            throw DataException("Error - DataExpanded:: opening of netCDF file for output failed.");
674       if (!dataFile.add_att("type_id",2) )
675            throw DataException("Error - DataExpanded:: appending data type to netCDF file failed.");
676       if (!dataFile.add_att("rank",rank) )
677            throw DataException("Error - DataExpanded:: appending rank attribute to netCDF file failed.");
678       if (!dataFile.add_att("function_space_type",type))
679            throw DataException("Error - DataExpanded:: appending function space attribute to netCDF file failed.");
680       ndims=rank+2;
681       if ( rank >0 ) {
682           dims[0]=shape[0];
683           if (! (ncdims[0] = dataFile.add_dim("d0",shape[0])) )
684                throw DataException("Error - DataExpanded:: appending ncdimsion 0 to netCDF file failed.");
685       }
686       if ( rank >1 ) {
687           dims[1]=shape[1];
688           if (! (ncdims[1] = dataFile.add_dim("d1",shape[1])) )
689                throw DataException("Error - DataExpanded:: appending ncdimsion 1 to netCDF file failed.");
690       }
691       if ( rank >2 ) {
692           dims[2]=shape[2];
693           if (! (ncdims[2] = dataFile.add_dim("d2", shape[2])) )
694                throw DataException("Error - DataExpanded:: appending ncdimsion 2 to netCDF file failed.");
695       }
696       if ( rank >3 ) {
697           dims[3]=shape[3];
698           if (! (ncdims[3] = dataFile.add_dim("d3", shape[3])) )
699                throw DataException("Error - DataExpanded:: appending ncdimsion 3 to netCDF file failed.");
700       }
701       dims[rank]=getFunctionSpace().getNumDataPointsPerSample();
702       if (! (ncdims[rank] = dataFile.add_dim("num_data_points_per_sample", dims[rank])) )
703                throw DataException("Error - DataExpanded:: appending num_data_points_per_sample to netCDF file failed.");
704       dims[rank+1]=getFunctionSpace().getNumSamples();
705       if (! (ncdims[rank+1] = dataFile.add_dim("num_samples", dims[rank+1])) )
706                throw DataException("Error - DataExpanded:: appending num_sample to netCDF file failed.");
707    
708       if (! ( ids = dataFile.add_var("id", ncInt, ncdims[rank+1])) )
709            throw DataException("Error - DataExpanded:: appending reference id to netCDF file failed.");
710       const int* ids_p=getFunctionSpace().borrowSampleReferenceIDs();
711       if (! (ids->put(ids_p,dims[rank+1])) )
712            throw DataException("Error - DataExpanded:: copy reference id  to netCDF buffer failed.");
713    
714       if (! ( var = dataFile.add_var("data", ncDouble, ndims, ncdims)) )
715            throw DataException("Error - DataExpanded:: appending variable to netCDF file failed.");
716       if (! (var->put(d_ptr,dims)) )
717            throw DataException("Error - DataExpanded:: copy data to netCDF buffer failed.");
718       #else
719       throw DataException("Error - DataExpanded:: dump is not configured with netCDF. Please contact your installation manager.");
720       #endif
721    }
722    
723    void
724    DataExpanded::setTaggedValue(int tagKey,
725                                 const DataArrayView& value)
726    {
727      int numSamples = getNumSamples();
728      int numDataPointsPerSample = getNumDPPSample();
729      int sampleNo,dataPointNo, i;
730      DataArrayView& thisView=getPointDataView();
731      DataArrayView::ValueType::size_type n = thisView.noValues();
732      double* p,*in=&(value.getData()[0]);
733      
734      if (value.noValues() != n) {
735        throw DataException("Error - DataExpanded::setTaggedValue: number of input values does not match number of values per data points.");
736      }
737    
738      #pragma omp parallel for private(sampleNo,dataPointNo,p,i) schedule(static)
739      for (sampleNo = 0; sampleNo < numSamples; sampleNo++) {
740        if (getFunctionSpace().getTagFromSampleNo(sampleNo) == tagKey ) {
741            for (dataPointNo = 0; dataPointNo < numDataPointsPerSample; dataPointNo++) {
742                p=&(m_data[getPointOffset(sampleNo,dataPointNo)]);
743                for (int i=0; i<n ;++i) p[i]=in[i];
744            }
745        }
746      }
747    }
748    
749    
750  }  // end of namespace  }  // end of namespace

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